Psyllid ID: psy3653

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200--
Protein Sequence
MYHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG
Secondary Structure (PSIPRED)
cccccHHHHHHHccccccccEEEEccccccccccccccccccccccccEEEccccccHHHHHcccccccccccccccccEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHHHccccccccccccccccEEEcccccccccccccccccccccccEEEcccccccHHHHHHHHc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHcccccccHHEEEcccccccccEEEHHcccccccccEEEcccccccHHHHHHHHcHHHcccccccccHHHHHcccccccccEEEHHcccccccccEEEcccccccHHHcccccEEccccccccHHHHHHHccccHcccccccccHHHHHcccccccccEEEEEcccccccccEEccccccccHHHHHHHHc
Coil and Loop (DISEMBL)
myhihvlffddhfslRCFQKCVTALEKtwhtehffcaqcgkqfgedgfhekdgkpycrddyfdlfapkcggcnrAIMENYVSALNTqwhstcfvcrdckkpvtgksfyamegkpdcrqpfqggsffdheglpycethyhakrgslcagchkpitgRCITAMFRKFHPEHFVCAFCLRqlnkgtfkeqndkpychgcfeklfg
Flexible Loop (DISEMBL)
MYHIHVLffddhfslRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGtfkeqndkpyCHGCFEKLFG
Low Complexity Region (SEG)
MYHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG
Disordered region (IsUnstruct)
*YHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEK***
Disordered Region (DISOPRED)
MYHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG
Disordered Region (DISEMBL)
MYHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG
Disordered Region (DISPRO)
MYHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYHIHVLFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	202	2.2.26 [Sep-21-2011]
Q66H76	586	Paxillin OS=Rattus norveg	yes	N/A	0.846	0.291	0.673	6e-74
Q8VI36	591	Paxillin OS=Mus musculus	yes	N/A	0.846	0.289	0.673	7e-74
P49023	591	Paxillin OS=Homo sapiens	no	N/A	0.866	0.296	0.66	1e-73
P49024	559	Paxillin OS=Gallus gallus	yes	N/A	0.866	0.313	0.66	1e-73
Q5R7I1	591	Paxillin OS=Pongo abelii	yes	N/A	0.846	0.289	0.673	2e-73
O60711	386	Leupaxin OS=Homo sapiens	no	N/A	0.846	0.443	0.571	5e-60
Q2TCH4	506	Transforming growth facto	N/A	N/A	0.841	0.335	0.569	5e-59
Q9N261	386	Leupaxin OS=Oryctolagus c	no	N/A	0.851	0.445	0.558	6e-59
Q99PD6	461	Transforming growth facto	no	N/A	0.861	0.377	0.532	5e-58
Q62219	461	Transforming growth facto	no	N/A	0.861	0.377	0.532	5e-58

>sp|Q66H76|PAXI_RAT Paxillin OS=Rattus norvegicus GN=Pxn PE=1 SV=1

 Score =  276 bits (706), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 132/196 (67%), Positives = 146/196 (74%), Gaps = 25/196 (12%)

Query: 13  FSLRCF-------QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC+        K VTAL++TWH EHFFCAQCG  FG +GFHEKDGK YCR DYFD+F
Sbjct: 408 FSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDYFDMF 467

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           APKCGGC RAI+ENY+SALNT WH  CFVCR+C                    PF  GSF
Sbjct: 468 APKCGGCARAILENYISALNTLWHPECFVCREC------------------FTPFVNGSF 509

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
           F+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNKGTFK
Sbjct: 510 FEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAFCLKQLNKGTFK 569

Query: 186 EQNDKPYCHGCFEKLF 201
           EQNDKPYC  CF KLF
Sbjct: 570 EQNDKPYCQSCFLKLF 585

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).
Rattus norvegicus (taxid: 10116)

>sp|Q8VI36|PAXI_MOUSE Paxillin OS=Mus musculus GN=Pxn PE=1 SV=1

 Score =  276 bits (706), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 132/196 (67%), Positives = 146/196 (74%), Gaps = 25/196 (12%)

Query: 13  FSLRCF-------QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC+        K VTAL++TWH EHFFCAQCG  FG +GFHEKDGK YCR DYFD+F
Sbjct: 413 FSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDYFDMF 472

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           APKCGGC RAI+ENY+SALNT WH  CFVCR+C                    PF  GSF
Sbjct: 473 APKCGGCARAILENYISALNTLWHPECFVCREC------------------FTPFVNGSF 514

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
           F+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNKGTFK
Sbjct: 515 FEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAFCLKQLNKGTFK 574

Query: 186 EQNDKPYCHGCFEKLF 201
           EQNDKPYC  CF KLF
Sbjct: 575 EQNDKPYCQSCFVKLF 590

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).

Mus musculus (taxid: 10090)

>sp|P49023|PAXI_HUMAN Paxillin OS=Homo sapiens GN=PXN PE=1 SV=3

 Score =  275 bits (704), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 132/200 (66%), Positives = 148/200 (74%), Gaps = 25/200 (12%)

Query: 9   FDDHFSLRCF-------QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC+        K VTAL++TWH EHFFCAQCG  FG +GFHEKDGK YCR DY
Sbjct: 409 YHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 468

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
           FD+FAPKCGGC RAI+ENY+SALNT WH  CFVCR+C                    PF 
Sbjct: 469 FDMFAPKCGGCARAILENYISALNTLWHPECFVCREC------------------FTPFV 510

Query: 122 GGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNK 181
            GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNK
Sbjct: 511 NGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAFCLKQLNK 570

Query: 182 GTFKEQNDKPYCHGCFEKLF 201
           GTFKEQNDKPYC  CF KLF
Sbjct: 571 GTFKEQNDKPYCQNCFLKLF 590

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).

Homo sapiens (taxid: 9606)

>sp|P49024|PAXI_CHICK Paxillin OS=Gallus gallus GN=PXN PE=1 SV=1

 Score =  275 bits (704), Expect = 1e-73,   Method: Compositional matrix adjust.
 Identities = 132/200 (66%), Positives = 148/200 (74%), Gaps = 25/200 (12%)

Query: 9   FDDHFSLRCF-------QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC+        K VTAL++TWH EHFFCAQCG  FG +GFHEKDGK YCR DY
Sbjct: 377 YHNLFSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGVFFGPEGFHEKDGKAYCRKDY 436

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
           FD+FAPKCGGC RAI+ENY+SALNT WH  CFVCR+C                    PF 
Sbjct: 437 FDMFAPKCGGCARAILENYISALNTLWHPECFVCREC------------------FTPFI 478

Query: 122 GGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNK 181
            GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNK
Sbjct: 479 NGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNK 538

Query: 182 GTFKEQNDKPYCHGCFEKLF 201
           GTFKEQNDKPYC  CF KLF
Sbjct: 539 GTFKEQNDKPYCQNCFLKLF 558

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion). Binds in vitro to vinculin as well as to the SH3 domain of c-SRC and, when tyrosine phosphorylated, to the SH2 domain of v-CRK.

Gallus gallus (taxid: 9031)

>sp|Q5R7I1|PAXI_PONAB Paxillin OS=Pongo abelii GN=PXN PE=2 SV=1

 Score =  275 bits (703), Expect = 2e-73,   Method: Compositional matrix adjust.
 Identities = 132/196 (67%), Positives = 146/196 (74%), Gaps = 25/196 (12%)

Query: 13  FSLRCF-------QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC+        K VTAL++TWH EHFFCAQCG  FG +GFHEKDGK YCR DYFD+F
Sbjct: 413 FSPRCYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDYFDMF 472

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           APKCGGC RAI+ENY+SALNT WH  CFVCR+C                    PF  GSF
Sbjct: 473 APKCGGCARAILENYISALNTLWHPECFVCREC------------------FTPFVNGSF 514

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
           F+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNKGTFK
Sbjct: 515 FEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAFCLKQLNKGTFK 574

Query: 186 EQNDKPYCHGCFEKLF 201
           EQNDKPYC  CF KLF
Sbjct: 575 EQNDKPYCQNCFLKLF 590

Cytoskeletal protein involved in actin-membrane attachment at sites of cell adhesion to the extracellular matrix (focal adhesion).

Pongo abelii (taxid: 9601)

>sp|O60711|LPXN_HUMAN Leupaxin OS=Homo sapiens GN=LPXN PE=1 SV=1

 Score =  230 bits (586), Expect = 5e-60,   Method: Compositional matrix adjust.
 Identities = 112/196 (57%), Positives = 136/196 (69%), Gaps = 25/196 (12%)

Query: 13  FSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC         K +TA+ +TWH EHFFC+ CG+ FG +GFHEKD KPYCR D+  +F
Sbjct: 207 FSPRCAYCAAPILDKVLTAMNQTWHPEHFFCSHCGEVFGAEGFHEKDKKPYCRKDFLAMF 266

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           +PKCGGCNR ++ENY+SA++T WH  CFVC DC        F +          F  GSF
Sbjct: 267 SPKCGGCNRPVLENYLSAMDTVWHPECFVCGDC--------FTS----------FSTGSF 308

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
           F+ +G P+CE HYH +RG+LC GC +PITGRCI+AM  KFHPEHFVCAFCL QL+KG F+
Sbjct: 309 FELDGRPFCELHYHHRRGTLCHGCGQPITGRCISAMGYKFHPEHFVCAFCLTQLSKGIFR 368

Query: 186 EQNDKPYCHGCFEKLF 201
           EQNDK YC  CF KLF
Sbjct: 369 EQNDKTYCQPCFNKLF 384

Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling.

Homo sapiens (taxid: 9606)

>sp|Q2TCH4|TGFI1_XENLA Transforming growth factor beta-1-induced transcript 1 protein OS=Xenopus laevis GN=tgfb1i1 PE=1 SV=2

 Score =  227 bits (578), Expect = 5e-59,   Method: Compositional matrix adjust.
 Identities = 107/188 (56%), Positives = 125/188 (66%), Gaps = 18/188 (9%)

Query: 15  LRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNR 74
           L   Q  VTAL  TWH EHF C  C K  GE+GFHEKDG+ YC DDYF LF   C GC  
Sbjct: 337 LPIVQNMVTALGCTWHPEHFCCKVCKKPIGEEGFHEKDGEQYCSDDYFRLFGAVCAGCTE 396

Query: 75  AIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYC 134
           A+ E+Y+SAL   WH  CFVC  C                    PF  GSFF+HEGLP C
Sbjct: 397 AVKESYISALGGLWHPQCFVCHVC------------------HTPFINGSFFEHEGLPLC 438

Query: 135 ETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCH 194
           ETHYH++RGSLCAGC +PITGRC+TAM +KFHP+H  C FCLRQLNKGTF+E ++KPYC 
Sbjct: 439 ETHYHSRRGSLCAGCEQPITGRCVTAMGKKFHPQHLNCTFCLRQLNKGTFREHDEKPYCQ 498

Query: 195 GCFEKLFG 202
            C+ +L+G
Sbjct: 499 ACYARLYG 506

Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. May regulate both Wnt and steroid signaling pathways and play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA-binding activity.

Xenopus laevis (taxid: 8355)

>sp|Q9N261|LPXN_RABIT Leupaxin OS=Oryctolagus cuniculus GN=LPXN PE=2 SV=1

 Score =  226 bits (577), Expect = 6e-59,   Method: Compositional matrix adjust.
 Identities = 110/197 (55%), Positives = 134/197 (68%), Gaps = 25/197 (12%)

Query: 13  FSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC         K +TA+ +TWH EHFFC+ CG+ FG +GFHEKD KPYCR D+  +F
Sbjct: 207 FSPRCAYCAAPILDKVLTAMNQTWHPEHFFCSHCGEVFGTEGFHEKDKKPYCRKDFLAMF 266

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           +PKCGGCNR ++ENY+SA+NT WH  CFVC DC    +  SF+ +EG+            
Sbjct: 267 SPKCGGCNRPVLENYLSAMNTVWHPECFVCGDCFSSFSTGSFFELEGR------------ 314

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
                 P+CE HYH +RG+LC GC +PITGRCI+AM  KFHPEHFVCAFCL QL+KG F+
Sbjct: 315 ------PFCELHYHQRRGTLCHGCGQPITGRCISAMGHKFHPEHFVCAFCLTQLSKGVFR 368

Query: 186 EQNDKPYCHGCFEKLFG 202
           EQNDK YC  CF KLF 
Sbjct: 369 EQNDKTYCQPCFNKLFS 385

Transcriptional coactivator for androgen receptor (AR) and serum response factor (SRF). Contributes to the regulation of cell adhesion, spreading and cell migration and acts as a negative regulator in integrin-mediated cell adhesion events. Suppresses the integrin-induced tyrosine phosphorylation of paxillin (PXN). May play a critical role as an adapter protein in the formation of the adhesion zone in osteoclasts. Negatively regulates B-cell antigen receptor (BCR) signaling.

Oryctolagus cuniculus (taxid: 9986)

>sp|Q99PD6|TGFI1_RAT Transforming growth factor beta-1-induced transcript 1 protein OS=Rattus norvegicus GN=Tgfb1i1 PE=1 SV=2

 Score =  223 bits (569), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 106/199 (53%), Positives = 131/199 (65%), Gaps = 25/199 (12%)

Query: 11  DHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFD 63
           + FS RC         K VTAL   WH EHF C  CG+ FGE+GFHE++G+PYCR D+  
Sbjct: 281 ERFSPRCGFCNQPIRHKMVTALGTHWHPEHFCCVSCGEPFGEEGFHEREGRPYCRRDFLQ 340

Query: 64  LFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGG 123
           LFAP+C GC   I++NY+SAL+  WH  CFVCR+C  P                  F GG
Sbjct: 341 LFAPRCQGCQGPILDNYISALSALWHPDCFVCRECLAP------------------FSGG 382

Query: 124 SFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT 183
           SFF+HEG P CE H+HA+RGSLCA C  P+TGRC++A+ R+FHP+HF C FCLR L KG+
Sbjct: 383 SFFEHEGRPLCENHFHAQRGSLCATCGLPVTGRCVSALGRRFHPDHFTCTFCLRPLTKGS 442

Query: 184 FKEQNDKPYCHGCFEKLFG 202
           F+E+  KPYC  CF KLFG
Sbjct: 443 FQERASKPYCQPCFLKLFG 461

Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. Links various intracellular signaling modules to plasma membrane receptors and regulates the Wnt and TGFB signaling pathways. May also regulate SLC6A3 and SLC6A4 targeting to the plasma membrane hence regulating their activity. In the nucleus, functions as a nuclear receptor coactivator regulating glucocorticoid, androgen, mineralocorticoid and progesterone receptor transcriptional activity. May play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA-binding activity.

Rattus norvegicus (taxid: 10116)

>sp|Q62219|TGFI1_MOUSE Transforming growth factor beta-1-induced transcript 1 protein OS=Mus musculus GN=Tgfb1i1 PE=1 SV=2

 Score =  223 bits (569), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 106/199 (53%), Positives = 131/199 (65%), Gaps = 25/199 (12%)

Query: 11  DHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFD 63
           + FS RC         K VTAL   WH EHF C  CG+ FGE+GFHE++G+PYCR D+  
Sbjct: 281 ERFSPRCGFCNQPIRHKMVTALGTHWHPEHFCCVSCGEPFGEEGFHEREGRPYCRRDFLQ 340

Query: 64  LFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGG 123
           LFAP+C GC   I++NY+SAL+  WH  CFVCR+C  P                  F GG
Sbjct: 341 LFAPRCQGCQGPILDNYISALSALWHPDCFVCRECLAP------------------FSGG 382

Query: 124 SFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT 183
           SFF+HEG P CE H+HA+RGSLCA C  P+TGRC++A+ R+FHP+HF C FCLR L KG+
Sbjct: 383 SFFEHEGRPLCENHFHAQRGSLCATCGLPVTGRCVSALGRRFHPDHFTCTFCLRPLTKGS 442

Query: 184 FKEQNDKPYCHGCFEKLFG 202
           F+E+  KPYC  CF KLFG
Sbjct: 443 FQERASKPYCQPCFLKLFG 461

Functions as a molecular adapter coordinating multiple protein-protein interactions at the focal adhesion complex and in the nucleus. Links various intracellular signaling modules to plasma membrane receptors and regulates the Wnt and TGFB signaling pathways. May also regulate SLC6A3 and SLC6A4 targeting to the plasma membrane hence regulating their activity. In the nucleus, functions as a nuclear receptor coactivator regulating glucocorticoid, androgen, mineralocorticoid and progesterone receptor transcriptional activity. May play a role in the processes of cell growth, proliferation, migration, differentiation and senescence. May have a zinc-dependent DNA-binding activity.

Mus musculus (taxid: 10090)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	202
380025706	607	PREDICTED: paxillin-like isoform 2 [Apis	0.940	0.313	0.817	1e-99
350421197	607	PREDICTED: paxillin-like [Bombus impatie	0.960	0.319	0.802	1e-99
340714019	605	PREDICTED: paxillin-like [Bombus terrest	0.960	0.320	0.802	1e-99
383863879	607	PREDICTED: paxillin-like [Megachile rotu	0.960	0.319	0.799	2e-99
332023566	607	Paxillin [Acromyrmex echinatior]	0.940	0.313	0.812	3e-99
307174007	610	Paxillin [Camponotus floridanus]	0.960	0.318	0.797	6e-99
307192546	621	Paxillin [Harpegnathos saltator]	0.960	0.312	0.792	1e-98
198473362	632	GA16481 [Drosophila pseudoobscura pseudo	0.940	0.300	0.842	2e-98
195164650	639	GL21108 [Drosophila persimilis] gi|19410	0.940	0.297	0.842	2e-98
195432836	630	GK23838 [Drosophila willistoni] gi|19416	0.940	0.301	0.826	4e-97

>gi|380025706|ref|XP_003696609.1| PREDICTED: paxillin-like isoform 2 [Apis florea]

 Score =  367 bits (943), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 175/214 (81%), Positives = 184/214 (85%), Gaps = 24/214 (11%)

Query: 13  FSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC         KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DYFD+F
Sbjct: 394 FSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDYFDMF 453

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP----------- 114
           APKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEGKP           
Sbjct: 454 APKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGKPVCPKCVGVDDD 513

Query: 115 ------DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPE 168
                 DCRQ FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPE
Sbjct: 514 EEEEEEDCRQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPE 573

Query: 169 HFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           HFVCAFCL+QLNKGTFKEQNDKPYCHGCF+KLFG
Sbjct: 574 HFVCAFCLKQLNKGTFKEQNDKPYCHGCFDKLFG 607

Source: Apis florea

Species: Apis florea

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350421197|ref|XP_003492766.1| PREDICTED: paxillin-like [Bombus impatiens]

 Score =  367 bits (942), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 175/218 (80%), Positives = 186/218 (85%), Gaps = 24/218 (11%)

Query: 9   FDDHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC         KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DY
Sbjct: 390 YHNLFSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDY 449

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP------- 114
           FD+FAPKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEGKP       
Sbjct: 450 FDMFAPKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGKPVCPKCVG 509

Query: 115 ----------DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRK 164
                     DCRQ FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRK
Sbjct: 510 VDDDEEEEEEDCRQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRK 569

Query: 165 FHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           FHPEHFVCAFCL+QLNKGTFKEQNDKPYCHGCF+KLFG
Sbjct: 570 FHPEHFVCAFCLKQLNKGTFKEQNDKPYCHGCFDKLFG 607

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714019|ref|XP_003395530.1| PREDICTED: paxillin-like [Bombus terrestris]

 Score =  367 bits (942), Expect = 1e-99,   Method: Compositional matrix adjust.
 Identities = 175/218 (80%), Positives = 186/218 (85%), Gaps = 24/218 (11%)

Query: 9   FDDHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC         KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DY
Sbjct: 388 YHNLFSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDY 447

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP------- 114
           FD+FAPKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEGKP       
Sbjct: 448 FDMFAPKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGKPVCPKCVG 507

Query: 115 ----------DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRK 164
                     DCRQ FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRK
Sbjct: 508 VDDDEEEEEEDCRQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRK 567

Query: 165 FHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           FHPEHFVCAFCL+QLNKGTFKEQNDKPYCHGCF+KLFG
Sbjct: 568 FHPEHFVCAFCLKQLNKGTFKEQNDKPYCHGCFDKLFG 605

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383863879|ref|XP_003707407.1| PREDICTED: paxillin-like [Megachile rotundata]

 Score =  367 bits (941), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 175/219 (79%), Positives = 186/219 (84%), Gaps = 25/219 (11%)

Query: 9   FDDHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC         KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DY
Sbjct: 389 YHNLFSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDY 448

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP------- 114
           FD+FAPKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEGKP       
Sbjct: 449 FDMFAPKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGKPVCPKCVG 508

Query: 115 -----------DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFR 163
                      DCRQ FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFR
Sbjct: 509 VDDDEEEEEEEDCRQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFR 568

Query: 164 KFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           KFHPEHFVCAFCL+QLNKGTFKEQNDKPYCHGCF+KLFG
Sbjct: 569 KFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHGCFDKLFG 607

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332023566|gb|EGI63802.1| Paxillin [Acromyrmex echinatior]

 Score =  366 bits (939), Expect = 3e-99,   Method: Compositional matrix adjust.
 Identities = 173/213 (81%), Positives = 183/213 (85%), Gaps = 23/213 (10%)

Query: 13  FSLRC------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA 66
           FS RC       +KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DYFD+FA
Sbjct: 395 FSPRCAYCNGPIRKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDYFDMFA 454

Query: 67  PKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC---------- 116
           PKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEG+P C          
Sbjct: 455 PKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGQPVCPKCVGVDDDD 514

Query: 117 -------RQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEH 169
                   Q FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEH
Sbjct: 515 EEEEEQEAQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEH 574

Query: 170 FVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           FVCAFCL+QLNKGTFKEQNDKPYCHGCFEKLFG
Sbjct: 575 FVCAFCLKQLNKGTFKEQNDKPYCHGCFEKLFG 607

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307174007|gb|EFN64717.1| Paxillin [Camponotus floridanus]

 Score =  365 bits (937), Expect = 6e-99,   Method: Compositional matrix adjust.
 Identities = 173/217 (79%), Positives = 184/217 (84%), Gaps = 23/217 (10%)

Query: 9   FDDHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC         KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DY
Sbjct: 394 YHNLFSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDY 453

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC----- 116
           FD+FAPKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEG+P C     
Sbjct: 454 FDMFAPKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGQPVCPKCVG 513

Query: 117 -----------RQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF 165
                       Q FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF
Sbjct: 514 VDDDEEEEEQEAQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF 573

Query: 166 HPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           HPEHFVCAFCL+QLNKGTFKEQNDKPYCHGCFEKLFG
Sbjct: 574 HPEHFVCAFCLKQLNKGTFKEQNDKPYCHGCFEKLFG 610

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307192546|gb|EFN75734.1| Paxillin [Harpegnathos saltator]

 Score =  364 bits (934), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 172/217 (79%), Positives = 184/217 (84%), Gaps = 23/217 (10%)

Query: 9   FDDHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           + + FS RC         KCVTALEKTWHTEHFFCAQCGKQFGE+GFHE+DGKPYCR+DY
Sbjct: 405 YHNLFSPRCAYCNGPILDKCVTALEKTWHTEHFFCAQCGKQFGEEGFHERDGKPYCREDY 464

Query: 62  FDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC----- 116
           FD+FAPKCGGCNRAIMENY+SALN+QWH  CFVCRDCKKPV+GKSFYAMEG+P C     
Sbjct: 465 FDMFAPKCGGCNRAIMENYISALNSQWHPDCFVCRDCKKPVSGKSFYAMEGQPVCPKCVG 524

Query: 117 -----------RQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF 165
                       Q FQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF
Sbjct: 525 VDDDEEEEEQEAQKFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF 584

Query: 166 HPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           HPEHFVCAFCL+QLNKGTFKEQNDKPYCHGCF+KLFG
Sbjct: 585 HPEHFVCAFCLKQLNKGTFKEQNDKPYCHGCFDKLFG 621

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198473362|ref|XP_001356270.2| GA16481 [Drosophila pseudoobscura pseudoobscura] gi|198139421|gb|EAL33333.2| GA16481 [Drosophila pseudoobscura pseudoobscura]

 Score =  363 bits (932), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 166/197 (84%), Positives = 179/197 (90%), Gaps = 7/197 (3%)

Query: 13  FSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC         KCVTAL+KTWHTEHFFCAQCG+QFGE+GFHE+DGKPYCR+DYF++F
Sbjct: 436 FSPRCAYCNGAILDKCVTALDKTWHTEHFFCAQCGQQFGEEGFHERDGKPYCRNDYFEMF 495

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           APKC GCNRAIMENY+SALN+QWH  CFVCRDCKK V GKSFYAMEGKPDCRQPFQGGSF
Sbjct: 496 APKCNGCNRAIMENYISALNSQWHPDCFVCRDCKKAVRGKSFYAMEGKPDCRQPFQGGSF 555

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
           FDHEGLPYCETHYHAKRGSLCAGC KPITGRCITAMF+KFHPEHFVCAFCL+QLNKGTFK
Sbjct: 556 FDHEGLPYCETHYHAKRGSLCAGCSKPITGRCITAMFKKFHPEHFVCAFCLKQLNKGTFK 615

Query: 186 EQNDKPYCHGCFEKLFG 202
           EQ DKPYCH CF+K+FG
Sbjct: 616 EQKDKPYCHVCFDKIFG 632

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195164650|ref|XP_002023159.1| GL21108 [Drosophila persimilis] gi|194105244|gb|EDW27287.1| GL21108 [Drosophila persimilis]

 Score =  363 bits (932), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 166/197 (84%), Positives = 179/197 (90%), Gaps = 7/197 (3%)

Query: 13  FSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC         KCVTAL+KTWHTEHFFCAQCG+QFGE+GFHE+DGKPYCR+DYF++F
Sbjct: 443 FSPRCAYCNGAILDKCVTALDKTWHTEHFFCAQCGQQFGEEGFHERDGKPYCRNDYFEMF 502

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           APKC GCNRAIMENY+SALN+QWH  CFVCRDCKK V GKSFYAMEGKPDCRQPFQGGSF
Sbjct: 503 APKCNGCNRAIMENYISALNSQWHPDCFVCRDCKKAVRGKSFYAMEGKPDCRQPFQGGSF 562

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK 185
           FDHEGLPYCETHYHAKRGSLCAGC KPITGRCITAMF+KFHPEHFVCAFCL+QLNKGTFK
Sbjct: 563 FDHEGLPYCETHYHAKRGSLCAGCSKPITGRCITAMFKKFHPEHFVCAFCLKQLNKGTFK 622

Query: 186 EQNDKPYCHGCFEKLFG 202
           EQ DKPYCH CF+K+FG
Sbjct: 623 EQKDKPYCHVCFDKIFG 639

Source: Drosophila persimilis

Species: Drosophila persimilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195432836|ref|XP_002064422.1| GK23838 [Drosophila willistoni] gi|194160507|gb|EDW75408.1| GK23838 [Drosophila willistoni]

 Score =  359 bits (921), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 167/202 (82%), Positives = 179/202 (88%), Gaps = 12/202 (5%)

Query: 13  FSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
           FS RC         KCVTALEKTWHTEHFFCAQCG+QFGE+GFHE+DGKPYCR+DYF++F
Sbjct: 429 FSPRCAYCNGAILDKCVTALEKTWHTEHFFCAQCGQQFGEEGFHERDGKPYCRNDYFEMF 488

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP-----DCRQPF 120
           APKC GCNRAIMENY+SALN+QWH  CFVCRDCKK V GKSFYAMEGKP     DCRQPF
Sbjct: 489 APKCNGCNRAIMENYISALNSQWHPDCFVCRDCKKAVRGKSFYAMEGKPVCPQCDCRQPF 548

Query: 121 QGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLN 180
           QGGSFFDHEGLPYCETHYHAKRGSLCAGC KPITGRCITAMF+KFHPEHFVCAFCL+QLN
Sbjct: 549 QGGSFFDHEGLPYCETHYHAKRGSLCAGCSKPITGRCITAMFKKFHPEHFVCAFCLKQLN 608

Query: 181 KGTFKEQNDKPYCHGCFEKLFG 202
           KGTFKEQ DKPYCH CF+K+FG
Sbjct: 609 KGTFKEQKDKPYCHACFDKIFG 630

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	202
FB|FBgn0041789	581	Pax "Paxillin" [Drosophila mel	0.435	0.151	0.920	3.2e-73
ZFIN|ZDB-GENE-040105-1	533	pxn "paxillin" [Danio rerio (t	0.430	0.163	0.793	7.7e-64
UNIPROTKB|F1MFD1	586	PXN "Uncharacterized protein"	0.430	0.148	0.793	1.3e-63
MGI|MGI:108295	591	Pxn "paxillin" [Mus musculus (	0.430	0.147	0.781	1.6e-63
UNIPROTKB|F1PUT6	590	PXN "Uncharacterized protein"	0.430	0.147	0.781	1.6e-63
UNIPROTKB|E7EMK8	403	PXN "Paxillin" [Homo sapiens (	0.430	0.215	0.781	1.6e-63
UNIPROTKB|F5GZ78	589	PXN "Paxillin" [Homo sapiens (	0.430	0.147	0.781	1.6e-63
UNIPROTKB|P49023	591	PXN "Paxillin" [Homo sapiens (	0.430	0.147	0.781	1.6e-63
RGD|1305759	586	Pxn "paxillin" [Rattus norvegi	0.430	0.148	0.781	2e-63
UNIPROTKB|F1M1Z5	591	Pxn "Paxillin" [Rattus norvegi	0.430	0.147	0.781	2e-63

FB|FBgn0041789 Pax "Paxillin" [Drosophila melanogaster (taxid:7227)]

 Score = 489 (177.2 bits), Expect = 3.2e-73, Sum P(2) = 3.2e-73
 Identities = 81/88 (92%), Positives = 85/88 (96%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGC KPITGRCITAMF+KFHPEHFVCAF
Sbjct:   494 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCSKPITGRCITAMFKKFHPEHFVCAF 553

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
             CL+QLNKGTFKEQ DKPYCH CF+K+FG
Sbjct:   554 CLKQLNKGTFKEQKDKPYCHTCFDKIFG 581

GO:0007016 "cytoskeletal anchoring at plasma membrane" evidence=ISS

GO:0005925 "focal adhesion" evidence=ISS;NAS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0035218 "leg disc development" evidence=IMP

GO:0032319 "regulation of Rho GTPase activity" evidence=IGI

GO:0035220 "wing disc development" evidence=IMP

GO:0010506 "regulation of autophagy" evidence=IGI

ZFIN|ZDB-GENE-040105-1 pxn "paxillin" [Danio rerio (taxid:7955)]

 Score = 416 (151.5 bits), Expect = 7.7e-64, Sum P(2) = 7.7e-64
 Identities = 69/87 (79%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+HEG PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   446 ECFTPFVNGSFFEHEGQPYCEAHYHERRGSLCSGCQKPITGRCITAMGKKFHPEHFVCAF 505

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   506 CLKQLNKGTFKEQNDKPYCQSCFVKLF 532

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0007519 "skeletal muscle tissue development" evidence=IGI

GO:0001756 "somitogenesis" evidence=IEP

GO:0009790 "embryo development" evidence=IEP

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F1MFD1 PXN "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 414 (150.8 bits), Expect = 1.3e-63, Sum P(2) = 1.3e-63
 Identities = 69/87 (79%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+HEG PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   499 ECFTPFVHGSFFEHEGQPYCEAHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 558

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   559 CLKQLNKGTFKEQNDKPYCQNCFLKLF 585

GO:0060396 "growth hormone receptor signaling pathway" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0030027 "lamellipodium" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA

GO:0008013 "beta-catenin binding" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

MGI|MGI:108295 Pxn "paxillin" [Mus musculus (taxid:10090)]

 Score = 414 (150.8 bits), Expect = 1.6e-63, Sum P(2) = 1.6e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   504 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 563

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   564 CLKQLNKGTFKEQNDKPYCQSCFVKLF 590

GO:0000187 "activation of MAPK activity" evidence=IDA

GO:0005178 "integrin binding" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005737 "cytoplasm" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005886 "plasma membrane" evidence=ISO

GO:0005925 "focal adhesion" evidence=ISO;IDA;TAS

GO:0006928 "cellular component movement" evidence=IMP

GO:0007010 "cytoskeleton organization" evidence=IMP

GO:0007155 "cell adhesion" evidence=IEA

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IMP;TAS

GO:0008013 "beta-catenin binding" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017166 "vinculin binding" evidence=ISO

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IDA

GO:0019901 "protein kinase binding" evidence=ISO

GO:0030027 "lamellipodium" evidence=ISO;IDA

GO:0030032 "lamellipodium assembly" evidence=IDA

GO:0030054 "cell junction" evidence=IEA

GO:0030159 "receptor signaling complex scaffold activity" evidence=TAS

GO:0031252 "cell leading edge" evidence=IDA

GO:0032403 "protein complex binding" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IDA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IDA

GO:0051435 "BH4 domain binding" evidence=IPI

GO:0060396 "growth hormone receptor signaling pathway" evidence=ISO

UNIPROTKB|F1PUT6 PXN "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 413 (150.4 bits), Expect = 1.6e-63, Sum P(2) = 1.6e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   503 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 562

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   563 CLKQLNKGTFKEQNDKPYCQNCFLKLF 589

GO:0060396 "growth hormone receptor signaling pathway" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0030027 "lamellipodium" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA

GO:0008013 "beta-catenin binding" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0005925 "focal adhesion" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005856 "cytoskeleton" evidence=IEA

UNIPROTKB|E7EMK8 PXN "Paxillin" [Homo sapiens (taxid:9606)]

 Score = 413 (150.4 bits), Expect = 1.6e-63, Sum P(2) = 1.6e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   316 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 375

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   376 CLKQLNKGTFKEQNDKPYCQNCFLKLF 402

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F5GZ78 PXN "Paxillin" [Homo sapiens (taxid:9606)]

 Score = 413 (150.4 bits), Expect = 1.6e-63, Sum P(2) = 1.6e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   502 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 561

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   562 CLKQLNKGTFKEQNDKPYCQNCFLKLF 588

GO:0005856 "cytoskeleton" evidence=IEA

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|P49023 PXN "Paxillin" [Homo sapiens (taxid:9606)]

 Score = 413 (150.4 bits), Expect = 1.6e-63, Sum P(2) = 1.6e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   504 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 563

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   564 CLKQLNKGTFKEQNDKPYCQNCFLKLF 590

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000187 "activation of MAPK activity" evidence=IEA

GO:0005178 "integrin binding" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA

GO:0007010 "cytoskeleton organization" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA

GO:0019901 "protein kinase binding" evidence=IEA

GO:0030032 "lamellipodium assembly" evidence=IEA

GO:0048041 "focal adhesion assembly" evidence=IEA

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA

GO:0051435 "BH4 domain binding" evidence=IEA

GO:0005938 "cell cortex" evidence=IEA

GO:0017166 "vinculin binding" evidence=IPI

GO:0005886 "plasma membrane" evidence=IDA;TAS

GO:0008013 "beta-catenin binding" evidence=IPI

GO:0005515 "protein binding" evidence=IPI

GO:0005875 "microtubule associated complex" evidence=TAS

GO:0007155 "cell adhesion" evidence=NAS

GO:0007172 "signal complex assembly" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0006936 "muscle contraction" evidence=TAS

GO:0007173 "epidermal growth factor receptor signaling pathway" evidence=TAS

GO:0034329 "cell junction assembly" evidence=TAS

GO:0005925 "focal adhesion" evidence=IDA

GO:0030027 "lamellipodium" evidence=IDA

GO:0034614 "cellular response to reactive oxygen species" evidence=IEP

GO:0060396 "growth hormone receptor signaling pathway" evidence=IDA

RGD|1305759 Pxn "paxillin" [Rattus norvegicus (taxid:10116)]

 Score = 413 (150.4 bits), Expect = 2.0e-63, Sum P(2) = 2.0e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   499 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 558

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   559 CLKQLNKGTFKEQNDKPYCQSCFLKLF 585

GO:0000187 "activation of MAPK activity" evidence=IEA;ISO

GO:0005178 "integrin binding" evidence=IPI

GO:0005856 "cytoskeleton" evidence=IEA

GO:0005886 "plasma membrane" evidence=IEA;ISO

GO:0005925 "focal adhesion" evidence=ISO;IDA

GO:0005938 "cell cortex" evidence=IEA

GO:0006928 "cellular component movement" evidence=IEA;ISO

GO:0007010 "cytoskeleton organization" evidence=IEA;ISO

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0007229 "integrin-mediated signaling pathway" evidence=IEA;ISO

GO:0008013 "beta-catenin binding" evidence=IEA;ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0017166 "vinculin binding" evidence=IEA;ISO

GO:0018108 "peptidyl-tyrosine phosphorylation" evidence=IEA;ISO

GO:0019901 "protein kinase binding" evidence=IPI

GO:0030027 "lamellipodium" evidence=IEA;ISO

GO:0030032 "lamellipodium assembly" evidence=IEA;ISO

GO:0031252 "cell leading edge" evidence=ISO

GO:0032403 "protein complex binding" evidence=IPI

GO:0034614 "cellular response to reactive oxygen species" evidence=IEA;ISO

GO:0048041 "focal adhesion assembly" evidence=IEA;ISO

GO:0048754 "branching morphogenesis of an epithelial tube" evidence=IEA;ISO

GO:0051435 "BH4 domain binding" evidence=IEA;ISO

GO:0060396 "growth hormone receptor signaling pathway" evidence=IEA;ISO

UNIPROTKB|F1M1Z5 Pxn "Paxillin" [Rattus norvegicus (taxid:10116)]

 Score = 413 (150.4 bits), Expect = 2.0e-63, Sum P(2) = 2.0e-63
 Identities = 68/87 (78%), Positives = 75/87 (86%)

Query:   115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAF 174
             +C  PF  GSFF+H+G PYCE HYH +RGSLC+GC KPITGRCITAM +KFHPEHFVCAF
Sbjct:   504 ECFTPFVNGSFFEHDGQPYCEVHYHERRGSLCSGCQKPITGRCITAMAKKFHPEHFVCAF 563

Query:   175 CLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             CL+QLNKGTFKEQNDKPYC  CF KLF
Sbjct:   564 CLKQLNKGTFKEQNDKPYCQSCFLKLF 590

GO:0005856 "cytoskeleton" evidence=IEA

GO:0007160 "cell-matrix adhesion" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P49024	PAXI_CHICK	No assigned EC number	0.66	0.8663	0.3130	yes	N/A
Q66H76	PAXI_RAT	No assigned EC number	0.6734	0.8465	0.2918	yes	N/A
Q8VI36	PAXI_MOUSE	No assigned EC number	0.6734	0.8465	0.2893	yes	N/A
Q5R7I1	PAXI_PONAB	No assigned EC number	0.6734	0.8465	0.2893	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	202
cd09411	52	cd09411, LIM4_Paxillin, The fourth LIM domain of P	1e-27
cd09339	52	cd09339, LIM4_Paxillin_like, The fourth LIM domain	3e-25
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	3e-23
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	5e-22
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	5e-21
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	5e-18
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	6e-15
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	1e-14
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	8e-14
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	2e-13
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	2e-12
pfam00412	58	pfam00412, LIM, LIM domain	4e-11
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	1e-10
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	2e-10
pfam00412	58	pfam00412, LIM, LIM domain	2e-10
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	1e-09
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	1e-09
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-09
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	5e-09
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	5e-09
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	2e-08
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	7e-08
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	9e-08
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	1e-07
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	1e-07
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-07
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-07
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	3e-07
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-07
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	5e-07
pfam00412	58	pfam00412, LIM, LIM domain	7e-07
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	7e-07
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	8e-07
cd09452	52	cd09452, LIM1_Enigma, The first LIM domain of Enig	9e-07
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-06
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	1e-06
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	1e-06
cd09429	53	cd09429, LIM3_FHL1, The third LIM domain of Four a	1e-06
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	2e-06
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	3e-06
cd09455	54	cd09455, LIM1_Enigma_like_1, The first LIM domain	3e-06
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	3e-06
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	3e-06
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	4e-06
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-06
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	5e-06
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	6e-06
cd09461	54	cd09461, LIM3_Enigma_like_1, The third LIM domain	8e-06
cd09339	52	cd09339, LIM4_Paxillin_like, The fourth LIM domain	9e-06
cd09430	52	cd09430, LIM5_LIMPETin, The fifth LIM domain of pr	1e-05
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	2e-05
cd09454	52	cd09454, LIM1_ZASP_Cypher, The first LIM domain of	2e-05
cd09411	52	cd09411, LIM4_Paxillin, The fourth LIM domain of P	3e-05
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	3e-05
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	3e-05
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	3e-05
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	4e-05
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	6e-05
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	7e-05
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	7e-05
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	9e-05
cd09458	55	cd09458, LIM3_Enigma, The third LIM domain of Enig	9e-05
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	9e-05
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	1e-04
cd09431	57	cd09431, LIM3_Fhl2, The third LIM domain of Four a	1e-04
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	1e-04
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	1e-04
cd09405	54	cd09405, LIM1_Paxillin, The first LIM domain of pa	2e-04
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	2e-04
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	2e-04
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	2e-04
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	2e-04
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	3e-04
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	3e-04
cd09460	55	cd09460, LIM3_ZASP_Cypher, The third LIM domain of	3e-04
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	4e-04
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	4e-04
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	5e-04
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	5e-04
cd09429	53	cd09429, LIM3_FHL1, The third LIM domain of Four a	6e-04
cd09328	56	cd09328, LIM2_abLIM, The second LIM domain on acti	6e-04
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	7e-04
cd09453	52	cd09453, LIM1_ENH, The first LIM domain of the Eni	7e-04
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	7e-04
cd09416	56	cd09416, LIM2_Testin, The second LIM domain of Tes	8e-04
cd09397	58	cd09397, LIM1_UF1, LIM domain in proteins of unkno	8e-04
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	0.001
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	0.001
cd09452	52	cd09452, LIM1_Enigma, The first LIM domain of Enig	0.001
cd09455	54	cd09455, LIM1_Enigma_like_1, The first LIM domain	0.001
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	0.001
cd09431	57	cd09431, LIM3_Fhl2, The third LIM domain of Four a	0.001
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	0.001
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.002
cd09430	52	cd09430, LIM5_LIMPETin, The fifth LIM domain of pr	0.002
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	0.002
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	0.002
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	0.002
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	0.002
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	0.003
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	0.003
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	0.003
cd09418	56	cd09418, LIM2_Prickle, The second LIM domain of Pr	0.003
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	0.004
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	0.004
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	0.004

>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin

 Score = 98.5 bits (245), Expect = 1e-27
 Identities = 46/52 (88%), Positives = 49/52 (94%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           C+GC KPITGRCITAM +KFHPEHFVCAFCL+QLNKGTFKEQNDKPYCH CF
Sbjct: 1   CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52

The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family

 Score = 92.4 bits (230), Expect = 3e-25
 Identities = 46/52 (88%), Positives = 49/52 (94%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CAGC KPITGRCITAM RKFHPEHFVCAFCL+QL+KGTFKEQ+DKPYCH CF
Sbjct: 1   CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 87.4 bits (217), Expect = 3e-23
 Identities = 41/71 (57%), Positives = 47/71 (66%), Gaps = 18/71 (25%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
           CGGCN+ I+ENY+SALNTQWH  CFVCR                  +C +PF  GSFF+H
Sbjct: 1   CGGCNKPILENYISALNTQWHPECFVCR------------------ECHKPFINGSFFEH 42

Query: 129 EGLPYCETHYH 139
           EGLPYCETHYH
Sbjct: 43  EGLPYCETHYH 53

The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin

 Score = 84.4 bits (209), Expect = 5e-22
 Identities = 37/52 (71%), Positives = 42/52 (80%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           C  C  PITGRCI+A+ RKFHPEHFVCAFCLR L +G+FKEQ+ KPYC  CF
Sbjct: 1   CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 81.7 bits (202), Expect = 5e-21
 Identities = 36/43 (83%), Positives = 40/43 (93%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           KCVTAL+KTWH EHFFCAQCGK FG++GFHEKDGKPYCR+DY
Sbjct: 10 DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin

 Score = 73.7 bits (181), Expect = 5e-18
 Identities = 38/71 (53%), Positives = 43/71 (60%), Gaps = 18/71 (25%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
           CGGC RAI+ENY+SALNT WH  CFVCR                  +C  PF  GSFF+H
Sbjct: 1   CGGCARAILENYISALNTLWHPECFVCR------------------ECFTPFVNGSFFEH 42

Query: 129 EGLPYCETHYH 139
           +G PYCE HYH
Sbjct: 43  DGQPYCEAHYH 53

The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin

 Score = 65.7 bits (160), Expect = 6e-15
 Identities = 32/42 (76%), Positives = 35/42 (83%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          K VTAL++TWH EHFFCAQCG  FG +GFHEKDGK YCR DY
Sbjct: 11 KVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 64.8 bits (158), Expect = 1e-14
 Identities = 26/43 (60%), Positives = 36/43 (83%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          Q  +TA+++TWH EHFFC+ CG+ FG++GF E+DGKPYCR D+
Sbjct: 10 QNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 62.7 bits (153), Expect = 8e-14
 Identities = 24/43 (55%), Positives = 29/43 (67%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
          + VTAL KTWH EHF CA+C  + G   F E+DG+PYC  DY 
Sbjct: 11 QVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53

The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 61.8 bits (150), Expect = 2e-13
 Identities = 32/71 (45%), Positives = 36/71 (50%), Gaps = 18/71 (25%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDH 128
           C GC R + ENY+SA N  WH  CFVC DC K                  PF  GSFF+ 
Sbjct: 1   CSGCGRPVKENYLSAANGVWHPECFVCSDCLK------------------PFTDGSFFEL 42

Query: 129 EGLPYCETHYH 139
           +G P CE HYH
Sbjct: 43  DGRPLCELHYH 53

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 59.3 bits (144), Expect = 2e-12
 Identities = 24/52 (46%), Positives = 34/52 (65%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CA C KPI G+ +TA+ + +HPEHFVCA C  +L    F E++ +PYC   +
Sbjct: 1   CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52

The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 55.8 bits (135), Expect = 4e-11
 Identities = 26/58 (44%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 146 CAGCHKPITGRCIT--AMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           CAGC KPI  R +   A+ + +HPE F CA C + L  G F E++ K YC   + KLF
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 54.6 bits (132), Expect = 1e-10
 Identities = 25/53 (47%), Positives = 35/53 (66%), Gaps = 1/53 (1%)

Query: 146 CAGCHKPITGRCI-TAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CAGC KPI GR +  A+ +K+HPE F C+ C + L   +F E++ KPYC  C+
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 53.9 bits (130), Expect = 2e-10
 Identities = 22/48 (45%), Positives = 31/48 (64%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           CA C+ PI  +C+TA+ + +HPEHF CA C +      F E++ KPYC
Sbjct: 1   CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYC 48

The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 54.3 bits (131), Expect = 2e-10
 Identities = 26/47 (55%), Positives = 28/47 (59%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF 65
          +    AL K WH E F CA CGK  G   F EKDGK YC+ DYF LF
Sbjct: 12 ELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH

 Score = 52.0 bits (125), Expect = 1e-09
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 144 SLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
            +C  C +PI GR +TA+ + +H EHFVCA C +        E+    YC
Sbjct: 1   PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYC 50

The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes. Length = 54

>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 51.8 bits (124), Expect = 1e-09
 Identities = 23/42 (54%), Positives = 30/42 (71%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          + VTAL +TWH EHF C QCGK+ G   F E++G+ YC +DY
Sbjct: 13 QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 50.8 bits (122), Expect = 3e-09
 Identities = 23/40 (57%), Positives = 26/40 (65%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          + AL K WH E F C+ CGK  G D F+EKDGKPYC   Y
Sbjct: 14 LRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH

 Score = 50.0 bits (120), Expect = 5e-09
 Identities = 21/44 (47%), Positives = 24/44 (54%)

Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
            + VTAL K WH EHF CA+C K F     +EK G  YC   Y
Sbjct: 11 EGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes. Length = 54

>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 50.3 bits (120), Expect = 5e-09
 Identities = 23/48 (47%), Positives = 32/48 (66%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           CA C KPI G+ +TA+ + +HPEHFVC  C ++L    F E+N + YC
Sbjct: 3   CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYC 50

The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin

 Score = 48.5 bits (115), Expect = 2e-08
 Identities = 22/49 (44%), Positives = 32/49 (65%)

Query: 145 LCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           +C  C KPI G+ +TAM + +HPEHFVC  C  ++    F E++ +PYC
Sbjct: 1   VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYC 49

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin

 Score = 47.3 bits (112), Expect = 7e-08
 Identities = 22/42 (52%), Positives = 28/42 (66%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          + VTA+ KTWH EHF C  C ++ G   F E+DG+PYC  DY
Sbjct: 12 QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 46.7 bits (111), Expect = 9e-08
 Identities = 22/52 (42%), Positives = 28/52 (53%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CA C  PI    +TAM + +HPEHF C+ C        F E++ KPYC   F
Sbjct: 1   CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 46.2 bits (110), Expect = 1e-07
 Identities = 18/48 (37%), Positives = 27/48 (56%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
           C  C + I+   V+AL   WH   FVC +CK  +  K+F+  +G+P C
Sbjct: 1   CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYC 48

The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 46.3 bits (110), Expect = 1e-07
 Identities = 19/38 (50%), Positives = 24/38 (63%)

Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          AL++TWH   F CA C +  G   FH +DG+PYC  DY
Sbjct: 15 ALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 45.8 bits (109), Expect = 2e-07
 Identities = 22/42 (52%), Positives = 26/42 (61%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDD 60
          ++ + AL K WH E F CA CGK    D F EKDGK YC+D 
Sbjct: 13 ERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 45.4 bits (108), Expect = 3e-07
 Identities = 22/51 (43%), Positives = 28/51 (54%), Gaps = 1/51 (1%)

Query: 69  CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
           C GC + I    +  AL  +WH  CF C  C KP+ G SFY  +GKP C +
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEK 51

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH

 Score = 45.0 bits (107), Expect = 3e-07
 Identities = 27/72 (37%), Positives = 32/72 (44%), Gaps = 18/72 (25%)

Query: 67  PKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFF 126
           P CG C R I    V+AL   WH   FVC  C+K                  PF G   +
Sbjct: 1   PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEK------------------PFLGHRHY 42

Query: 127 DHEGLPYCETHY 138
           + +GL YCETHY
Sbjct: 43  EKKGLAYCETHY 54

The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes. Length = 54

>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 45.0 bits (106), Expect = 4e-07
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           CG C R I+   ++AL   WH +CFVC  C  P+    F+  +G+P C   +
Sbjct: 1   CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 18/52 (34%), Positives = 30/52 (57%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  C++ I+   + AL   WH +CFVC  CK+P+    F+  +G+P C + +
Sbjct: 1   CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 44.3 bits (105), Expect = 7e-07
 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 69  CGGCNRAIMENYVS--ALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
           C GC + I +  +   AL   WH  CF C  C KP+    F+  +GK  C+  + 
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYF 55

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 44.3 bits (105), Expect = 7e-07
 Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 2/52 (3%)

Query: 68  KCGGCNRAIMEN--YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           KC GC + I      + AL   WH  CF C  C KP++G +F+  +GK  C+
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCK 52

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 44.2 bits (105), Expect = 8e-07
 Identities = 21/48 (43%), Positives = 28/48 (58%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           C GC+KPI    I+A+  ++HPE FVC  C +    G+F E    PYC
Sbjct: 1   CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYC 48

The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma

 Score = 44.0 bits (104), Expect = 9e-07
 Identities = 21/52 (40%), Positives = 32/52 (61%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CA C+K I GR + A+ R +HPE F C+ C + L++G F E+    +C  C+
Sbjct: 1   CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52

The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 25/53 (47%), Positives = 33/53 (62%), Gaps = 2/53 (3%)

Query: 146 CAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
           CAGC KPI G  R + A+ + +HPE F CA C + L+  TF E++ K YC  C
Sbjct: 2   CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 43.9 bits (104), Expect = 1e-06
 Identities = 19/52 (36%), Positives = 28/52 (53%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CA C++ I G  + A+ R +HPE F C+ C   L +  F E+    YC  C+
Sbjct: 1   CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 44.8 bits (106), Expect = 1e-06
 Identities = 20/52 (38%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 69  CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
           CG C + +   +  V AL   +H TCF C  C++ + G+ FY++EGKP C +
Sbjct: 34  CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEE 85

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 87

>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 43.6 bits (103), Expect = 1e-06
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
           C  CN+ I    V+  +  WHS CFVC  C K + G+ F A+E +  C
Sbjct: 1   CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48

The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like family

 Score = 43.6 bits (103), Expect = 2e-06
 Identities = 20/51 (39%), Positives = 30/51 (58%), Gaps = 2/51 (3%)

Query: 69  CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           C GC+  I   + ++ AL   WH TCFVC  C   + G++FY+ + KP C+
Sbjct: 1   CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCK 51

The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 42.4 bits (100), Expect = 3e-06
 Identities = 20/52 (38%), Positives = 29/52 (55%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  CN  I++  V+AL+  WH   F C  C KP   + F+  +GKP CR+ +
Sbjct: 1   CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma subfamily with unknown function

 Score = 42.8 bits (101), Expect = 3e-06
 Identities = 21/54 (38%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCA--FCLRQLNKGTFKEQNDKPYCHGCF 197
           C  C++ I G  ITA+ + + P+HF+CA   C R L    F E+  + YC  CF
Sbjct: 1   CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYCF 54

The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 42.7 bits (100), Expect = 3e-06
 Identities = 19/52 (36%), Positives = 26/52 (50%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  C + I    + AL   WH  CF C  CK P+  ++FY  EG P C + +
Sbjct: 1   CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 42.7 bits (101), Expect = 3e-06
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFG-EDGFHEKDGKPYCRDDY 61
           +TAL + +H EHF C+ C   FG  D ++E +GK YC   Y
Sbjct: 12 YITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 42.1 bits (99), Expect = 4e-06
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           C+GC +P+    ++A    +HPE FVC+ CL+    G+F E + +P C
Sbjct: 1   CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 17/40 (42%), Positives = 23/40 (57%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          + AL++TWH   F C  C      + FH +DG+PYC  DY
Sbjct: 13 INALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score = 42.2 bits (100), Expect = 5e-06
 Identities = 17/47 (36%), Positives = 21/47 (44%), Gaps = 1/47 (2%)

Query: 69  CGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP 114
           C GC   I    ++SAL   WH  CF C  C+KP+    F      P
Sbjct: 1   CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDP 47

The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 41.9 bits (99), Expect = 6e-06
 Identities = 17/39 (43%), Positives = 20/39 (51%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
           C  C + I   +V AL   +H  CF C DC KPV  K F
Sbjct: 1   CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKPVASKFF 39

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma subfamily with unknown function

 Score = 41.8 bits (98), Expect = 8e-06
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 78  ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           + +V ALN  +HS CF C  C   + G+SFYA  G+P C+
Sbjct: 12  DRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51

The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family

 Score = 41.2 bits (97), Expect = 9e-06
 Identities = 19/42 (45%), Positives = 27/42 (64%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          +C+TA+ + +H EHF CA C KQ  +  F E+D KPYC   +
Sbjct: 11 RCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 19/52 (36%), Positives = 26/52 (50%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  CN+ I    V+  N  WH  CF C +C K + G+ F + + KP C   F
Sbjct: 1   CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin

 Score = 40.5 bits (95), Expect = 2e-05
 Identities = 17/38 (44%), Positives = 25/38 (65%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
          +C++AL + +H EHF CA C +   +  F E+ GKPYC
Sbjct: 11 RCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48

The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher family

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           C  C+  I G  + A+ R +HPE F C +C   L   +F E+ +  YC  C+
Sbjct: 1   CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin

 Score = 39.9 bits (93), Expect = 3e-05
 Identities = 19/38 (50%), Positives = 26/38 (68%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
          +C+TA+ K +H EHF CA C KQ  +  F E++ KPYC
Sbjct: 11 RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYC 48

The fourth LIM domain of Paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 19/48 (39%), Positives = 26/48 (54%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           C GC + I    I+A+   +HPE FVC  C      G+F E + +PYC
Sbjct: 1   CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYC 48

The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CAGC   I  GR ++A+   +HPE F C  C + + +  F    + PY   C+
Sbjct: 1   CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 39.9 bits (94), Expect = 3e-05
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 146 CAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFE 198
           CA C + I +G    A  + +H +HF C  C   L    +  +  KPYC  C+E
Sbjct: 3   CAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56

The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 39.7 bits (93), Expect = 4e-05
 Identities = 15/39 (38%), Positives = 26/39 (66%)

Query: 82  SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           +A++  +H +CF C  C+  + GK FYA++GKP C + +
Sbjct: 16  TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 39.2 bits (92), Expect = 6e-05
 Identities = 21/52 (40%), Positives = 28/52 (53%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CA C K IT   +T   + +H E FVC  C +QL    F  +++ PYC  CF
Sbjct: 1   CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 38.8 bits (91), Expect = 7e-05
 Identities = 19/52 (36%), Positives = 26/52 (50%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  C +AI    V+  +  WH  CFVC  CKK + G+ F + +  P C   F
Sbjct: 1   CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 38.9 bits (91), Expect = 7e-05
 Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 2/50 (4%)

Query: 69  CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
           CG C   ++      +A++  +H  CF C  C   + G+ FYA+E K  C
Sbjct: 1   CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYC 50

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin

 Score = 38.4 bits (89), Expect = 9e-05
 Identities = 20/48 (41%), Positives = 27/48 (56%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           C  C+ PI  + +TA+ R +HPEHF CA C        F E++ K YC
Sbjct: 1   CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYC 48

The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma

 Score = 38.9 bits (90), Expect = 9e-05
 Identities = 21/51 (41%), Positives = 31/51 (60%), Gaps = 2/51 (3%)

Query: 69  CGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           C GC+  I   + ++ AL   WH TCFVC  C+  + GK+FY+ + KP C+
Sbjct: 1   CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCK 51

The third LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 38.5 bits (90), Expect = 9e-05
 Identities = 19/38 (50%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          AL+K WH   F C +CGK    + +  KDGKPYC  DY
Sbjct: 16 ALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52

The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 38.1 bits (89), Expect = 1e-04
 Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 1/50 (2%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKG-TFKEQNDKPYCH 194
           C  C   + G  ITA+ RK+H EHF C+ C        ++ E   K YCH
Sbjct: 1   CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCH 50

The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 22/57 (38%), Positives = 30/57 (52%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           C  C KPIT   +T   + +H E FVC  C +QL+   F  ++D  YC  CF  L+ 
Sbjct: 1   CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57

The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. Length = 57

>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 18/48 (37%), Positives = 29/48 (60%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA 66
          +K V +  + +H + F CAQC + F +  F+E +G+ YC  D+  LFA
Sbjct: 12 EKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 38.2 bits (89), Expect = 1e-04
 Identities = 23/53 (43%), Positives = 33/53 (62%), Gaps = 2/53 (3%)

Query: 69  CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C GC+R I++ ++ + L+  WH+ C  C DCK P+T K F + EGK  CR  F
Sbjct: 1   CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCRNDF 52

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 16/53 (30%), Positives = 29/53 (54%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQ 121
           CG C + I    V+A+   WH   FVC  C++ +  ++F+  +G+P C + + 
Sbjct: 2   CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight cons erved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 145 LCAGCHKPI--TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           LC  C +P+  T   + A+   FH   F C  C +QL    F     KPYC  C+
Sbjct: 33  LCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 87

>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 38.7 bits (90), Expect = 2e-04
 Identities = 17/43 (39%), Positives = 22/43 (51%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          Q  V AL   +H   F C QC +Q     F+  +GKPYC + Y
Sbjct: 45 QPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 87

>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4 family

 Score = 37.8 bits (88), Expect = 2e-04
 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)

Query: 69  CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFY 108
           CGGC   I++ ++   L+  WH+ C  C DC   +T K F 
Sbjct: 1   CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFA 41

The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 37.6 bits (87), Expect = 2e-04
 Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSF 107
           P C GCN+ I++ ++   L+  WHS C  C DC+  +  K F
Sbjct: 2   PLCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCF 43

The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 21/52 (40%), Positives = 26/52 (50%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           CG C   I    +SAL  ++H   FVC  C +P+T  SF    GKP C   F
Sbjct: 1   CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 37.1 bits (86), Expect = 3e-04
 Identities = 18/48 (37%), Positives = 27/48 (56%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           CA CHK I G  + A+ + +H   FVCA C + +    F  ++ +PYC
Sbjct: 1   CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYC 48

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher family

 Score = 37.3 bits (86), Expect = 3e-04
 Identities = 18/52 (34%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 69  CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
           C GC+  +   + ++ AL   WH TCF+C  C   + G+ FY+ + KP C++
Sbjct: 1   CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKK 52

The third LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 36.5 bits (85), Expect = 4e-04
 Identities = 17/40 (42%), Positives = 21/40 (52%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          ++AL   WH E F C +C K F    F E +G PYC   Y
Sbjct: 13 ISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 36.9 bits (86), Expect = 4e-04
 Identities = 20/53 (37%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 69  CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C GC + I       AL+ QWH  CF C++C K +TG+ +   +GKP C + +
Sbjct: 1   CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52

The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 36.8 bits (86), Expect = 5e-04
 Identities = 17/41 (41%), Positives = 22/41 (53%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
             A  K WH +HF C QC +  G   +  ++GKPYC D Y
Sbjct: 15 YTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55

The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 36.3 bits (84), Expect = 5e-04
 Identities = 18/41 (43%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYF 62
          V AL + WH + F C+ C      + + EKDGK YCR DY+
Sbjct: 14 VQALNQDWHCDCFRCSVC-SDSLSNWYFEKDGKLYCRKDYW 53

The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 36.3 bits (84), Expect = 6e-04
 Identities = 19/53 (35%), Positives = 29/53 (54%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFE 198
           C  C+KPIT   +T   + +H E FVC+ C ++L    F    D+ YC  C++
Sbjct: 1   CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM (abLIM) proteins

 Score = 36.2 bits (84), Expect = 6e-04
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 143 GSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPY-CHGC 196
           G+ C  C   + G  ++A+ + +HP+ FVC+ C +    G     N K   C  C
Sbjct: 1   GTKCDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKC 55

The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 16/38 (42%), Positives = 20/38 (52%)

Query: 24 ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          AL+ TWH   F CA C        F+ ++G PYC  DY
Sbjct: 15 ALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog (ENH) family

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 18/52 (34%), Positives = 27/52 (51%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           CA C++ I G  + A+ + +HPE F CA C   +    F E+    YC  C+
Sbjct: 1   CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52

The first LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH) family

 Score = 36.1 bits (83), Expect = 7e-04
 Identities = 19/52 (36%), Positives = 31/52 (59%), Gaps = 2/52 (3%)

Query: 69  CGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
           C GC   I   + ++ AL   WH TCFVC  C + + G++F++ + KP C++
Sbjct: 1   CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKK 52

The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188800 cd09416, LIM2_Testin, The second LIM domain of Testin

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 19/52 (36%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 67  PKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           P+C GC+  I  N Y  A N  WH   F C DC   + G+ +  +  KP C+
Sbjct: 1   PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCK 52

The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function

 Score = 36.1 bits (84), Expect = 8e-04
 Identities = 20/75 (26%), Positives = 25/75 (33%), Gaps = 21/75 (28%)

Query: 69  CGGCNRAIMENYVS----ALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGS 124
           C  C   I    +S     L+ QWH  CFVC  C  P                       
Sbjct: 1   CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSV-----------------P 43

Query: 125 FFDHEGLPYCETHYH 139
            +  +  PYC+ HYH
Sbjct: 44  CYVLDDKPYCQQHYH 58

The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 58

>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 17/52 (32%), Positives = 27/52 (51%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  C   I++N ++A++  WH   F C  C +    + F   +GKP CR+ F
Sbjct: 1   CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 15/36 (41%), Positives = 20/36 (55%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
          ++A    WH E F C+ C K F +  F E DG+P C
Sbjct: 13 LSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma

 Score = 35.2 bits (81), Expect = 0.001
 Identities = 15/36 (41%), Positives = 22/36 (61%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
          + AL +++H E F C+QC K   E GF E+ G  +C
Sbjct: 13 LVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFC 48

The first LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes such as mitogenic activity, insulin related actin organization, and glucose metabolism. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma subfamily with unknown function

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 16/38 (42%), Positives = 22/38 (57%), Gaps = 2/38 (5%)

Query: 22 VTALEKTWHTEHFFCA--QCGKQFGEDGFHEKDGKPYC 57
          +TAL K W  +HF CA   C +   + GF E+ G+ YC
Sbjct: 13 ITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYC 50

The first LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized members: Enigma, ENH and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the Enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 35.7 bits (83), Expect = 0.001
 Identities = 18/52 (34%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 67  PKCGGCNRAI-MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           P+C  C+  I    Y  A    WH   F C  C +P+ G+ +   EGKP C 
Sbjct: 1   PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCL 52

The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 35.7 bits (82), Expect = 0.001
 Identities = 17/52 (32%), Positives = 25/52 (48%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           C  C + I    V+  +  WH  CFVC  CKK ++G+ F + +    C   F
Sbjct: 1   CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCF 52

The third LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. Length = 57

>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 35.3 bits (81), Expect = 0.001
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTF-KEQNDKPYC 193
           CA C + IT R + A  + +HP+ F C  C   L   +F  +Q ++P+C
Sbjct: 1   CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHC 49

The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein. Length = 60

>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 15/36 (41%), Positives = 20/36 (55%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
          + AL ++WH E F C+ C     E GF E+ G  YC
Sbjct: 13 LVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYC 48

The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin

 Score = 35.1 bits (81), Expect = 0.002
 Identities = 18/52 (34%), Positives = 26/52 (50%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           C+ C+K I    +T     +H E F C  C + L    F  +++KPYC  CF
Sbjct: 1   CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 23 TALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          TA+++ +H   F C QC        F+  DGKPYC +DY
Sbjct: 16 TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 16/40 (40%), Positives = 20/40 (50%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          VT  ++ WH E F C  C KQ     F  +D  PYC D +
Sbjct: 13 VTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The third LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 18/62 (29%)

Query: 78  ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETH 137
           E  V++    +H  CFVC                    C QPF  G F++ EG  YCE  
Sbjct: 12  EKIVNSNGELYHEQCFVC------------------AQCFQPFPDGLFYEFEGRKYCEHD 53

Query: 138 YH 139
           + 
Sbjct: 54  FQ 55

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 35.0 bits (81), Expect = 0.002
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 146 CAGCHKPITGR-CITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           C  C KP+      T++ R +H     C  C + L  G   E   KPYC+ C+
Sbjct: 1   CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 14/40 (35%), Positives = 18/40 (45%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
           T+L + WH     C +C K        E +GKPYC   Y
Sbjct: 14 KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 34.6 bits (79), Expect = 0.003
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 1/41 (2%)

Query: 69  CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFY 108
           C GCN+ I++ ++   L+  WHS+C  C DC+  +  + F 
Sbjct: 1   CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFS 41

The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 34.9 bits (80), Expect = 0.003
 Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 67  PKCGGCNRAIM-ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPF 120
           P C  C ++I    Y+ ALN+ WH+ CF C +C   ++   +Y  +G+  C++ +
Sbjct: 20  PVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLS-HWYYEKDGRLFCKKDY 73

The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 74

>gnl|CDD|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 14/37 (37%), Positives = 21/37 (56%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYC 57
          C  A  + WH +HF C +C  Q G   +  ++G+PYC
Sbjct: 15 CTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51

The second LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Two forms of prickles have been identified; namely prickle 1 and prickle 2. Prickle 1 and prickle 2 are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin

 Score = 34.0 bits (78), Expect = 0.004
 Identities = 17/40 (42%), Positives = 21/40 (52%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          ++AL   WH E F C +C   F    F E DG+PYC   Y
Sbjct: 13 ISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52

The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH

 Score = 34.2 bits (79), Expect = 0.004
 Identities = 15/49 (30%), Positives = 21/49 (42%)

Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
           CG C   ++   + A+N  WH  CF C  C K +    F    G+  C 
Sbjct: 1   CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCH 49

The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 33.9 bits (78), Expect = 0.004
 Identities = 15/52 (28%), Positives = 30/52 (57%), Gaps = 2/52 (3%)

Query: 69  CGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGK-SFYAMEGKPDCRQ 118
           C GC   I + +   A++ QWH++C  C +C+ P+  + S ++ +G   C++
Sbjct: 1   CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKE 52

The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	202
KOG2272|consensus	332		100.0
KOG1701|consensus	468		100.0
KOG2272|consensus	332		99.97
KOG1044|consensus	670		99.94
KOG1703|consensus	479		99.93
KOG1044|consensus	670		99.89
KOG1701|consensus	468		99.88
KOG1703|consensus	479		99.85
KOG4577|consensus	383		99.78
KOG4577|consensus	383		99.76
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.61
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.37
KOG1700|consensus	200		99.25
KOG1700|consensus	200		99.13
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.8
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.55
KOG0490|consensus	235		97.48
KOG0490|consensus	235		97.3
KOG1702|consensus	264		97.07
KOG1702|consensus	264		96.62
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	91.59
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	91.03
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.21
KOG2462|consensus	279		82.76
PF07503	35	zf-HYPF: HypF finger; InterPro: IPR011125 Zinc fin	82.29
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	81.13
PF11781	36	RRN7: RNA polymerase I-specific transcription init	81.12

>KOG2272|consensus

Probab=100.00  E-value=3e-40  Score=253.63  Aligned_cols=194  Identities=34%  Similarity=0.731  Sum_probs=175.8

Q ss_pred             hHHhhCcCc------ccchhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCccccccccccccc
Q psy3653           9 FDDHFSLRC------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVS   82 (202)
Q Consensus         9 ~~~~~~~~C------~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~   82 (202)
                      ++...|.||      .++++...+..||.+||.|+.|-.|+.++.|++.+|+.||+.|+..+|+|-|..|++.|.+++|.
T Consensus        10 ~~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVik   89 (332)
T KOG2272|consen   10 LANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIK   89 (332)
T ss_pred             HHHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHH
Confidence            456789999      45788889999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCC----------------------------------------
Q psy3653          83 ALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG----------------------------------------  122 (202)
Q Consensus        83 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~----------------------------------------  122 (202)
                      +++.+||+.||+|..|++.|.+..|+...|+.+|+++-+.                                        
T Consensus        90 amnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C  169 (332)
T KOG2272|consen   90 AMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTC  169 (332)
T ss_pred             hhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceecccc
Confidence            9999999999999999999999999888888777544321                                        


Q ss_pred             -----CceeecCCCccccccccccCCCCCCCCCCCcccceeeecCcccccccccccccccccCCCceEeeCCcccChhhH
Q psy3653         123 -----GSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF  197 (202)
Q Consensus       123 -----~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~  197 (202)
                           +..-+..|.+||.+|+.+..-+.|..|.+||.+++|.++|+.||.++|+|+.|.+++-+-+.+++.|.+||..+|
T Consensus       170 ~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~  249 (332)
T KOG2272|consen  170 GKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY  249 (332)
T ss_pred             cccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHH
Confidence                 011123567899999998889999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhcC
Q psy3653         198 EKLFG  202 (202)
Q Consensus       198 ~~~fg  202 (202)
                      .+|||
T Consensus       250 ~qLfG  254 (332)
T KOG2272|consen  250 HQLFG  254 (332)
T ss_pred             HHHhh
Confidence            99998

>KOG1701|consensus

Probab=100.00  E-value=9.7e-37  Score=249.62  Aligned_cols=170  Identities=31%  Similarity=0.671  Sum_probs=154.3

Q ss_pred             hCcCcccc------hhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCc
Q psy3653          13 FSLRCFQK------CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNT   86 (202)
Q Consensus        13 ~~~~C~~~------~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~   86 (202)
                      .|.+|.+.      .+.||++.||..||+|.+|++.|.++.||..|+++||+.||.+.. .+|..|+++|.++++.|+|+
T Consensus       276 iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-ekC~~Cg~~I~d~iLrA~Gk  354 (468)
T KOG1701|consen  276 ICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-EKCNKCGEPIMDRILRALGK  354 (468)
T ss_pred             hhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-HHHhhhhhHHHHHHHHhccc
Confidence            78899543      478999999999999999999999999999999999999997754 69999999999999999999


Q ss_pred             eecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcc---cc----eee
Q psy3653          87 QWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPIT---GR----CIT  159 (202)
Q Consensus        87 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~---~~----~~~  159 (202)
                      .||+.||+|..|++.|++..|.+                 +.++++||..+|+++|+++|+.|++||.   |+    .|+
T Consensus       355 ayHp~CF~Cv~C~r~ldgipFtv-----------------d~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvv  417 (468)
T KOG1701|consen  355 AYHPGCFTCVVCARCLDGIPFTV-----------------DSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVV  417 (468)
T ss_pred             ccCCCceEEEEeccccCCccccc-----------------cCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEE
Confidence            99999999999999999988764                 6788999999999999999999999993   21    378


Q ss_pred             ecCcccccccccccccccccC----CCceEeeCCcccChhhHhhh
Q psy3653         160 AMFRKFHPEHFVCAFCLRQLN----KGTFKEQNDKPYCHGCFEKL  200 (202)
Q Consensus       160 ~~~~~~H~~Cf~C~~C~~~l~----~~~~~~~~~~~yC~~c~~~~  200 (202)
                      ++++.||.+|++|..|+..|+    +...+..||.++|+.|..+.
T Consensus       418 amdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~R  462 (468)
T KOG1701|consen  418 AMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKR  462 (468)
T ss_pred             EccccccccceehhhcCccccccCCCCcceeccCceeechhhhhh
Confidence            999999999999999999998    23389999999999998765

>KOG2272|consensus

Probab=99.97  E-value=1.4e-33  Score=216.92  Aligned_cols=164  Identities=34%  Similarity=0.829  Sum_probs=141.8

Q ss_pred             ccchhcccccccccccccccccccccCCCceeeeCCe-------------------------------------------
Q psy3653          18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGK-------------------------------------------   54 (202)
Q Consensus        18 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~-------------------------------------------   54 (202)
                      .|++|.||+.+||+.||+|..|++.|++..|+...|+                                           
T Consensus        84 iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yH  163 (332)
T KOG2272|consen   84 IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYH  163 (332)
T ss_pred             hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccc
Confidence            5788999999999999999999988877666544444                                           


Q ss_pred             --------------------eeccccccccCCCCCcccccccccccccccCceecccCCCCCCCCCCCCCCceeecCCcc
Q psy3653          55 --------------------PYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP  114 (202)
Q Consensus        55 --------------------~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~  114 (202)
                                          +||.+|+.+.-.|.|..|.++|.+++|.++|+.||.+.|+|+.|-+|+-+-         
T Consensus       164 FkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPFlGH---------  234 (332)
T KOG2272|consen  164 FKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPFLGH---------  234 (332)
T ss_pred             eecccccccccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcccch---------
Confidence                                455555554555778889999998899999999999999999998887654         


Q ss_pred             cCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccceeeecCcccccccccccccccccCCCc-eEeeCCcccC
Q psy3653         115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT-FKEQNDKPYC  193 (202)
Q Consensus       115 ~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~~~yC  193 (202)
                               ..+++.|.+||+++|.++++..|..|+.+|.|.++.|+++.|.++||+|+.|++.|...+ |++.|.+|.|
T Consensus       235 ---------rHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~C  305 (332)
T KOG2272|consen  235 ---------RHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVC  305 (332)
T ss_pred             ---------hhhhhcCchhHHHHHHHHhhhhheecCCccCccHHHHhhhhhccccccccccccccccccceeeeccchHH
Confidence                     345799999999999999999999999999999999999999999999999999998554 9999999999


Q ss_pred             hhhHhh
Q psy3653         194 HGCFEK  199 (202)
Q Consensus       194 ~~c~~~  199 (202)
                      +.||++
T Consensus       306 KkCy~r  311 (332)
T KOG2272|consen  306 KKCYDR  311 (332)
T ss_pred             HHHHhh
Confidence            999974

>KOG1044|consensus

Probab=99.94  E-value=1e-27  Score=202.78  Aligned_cols=175  Identities=25%  Similarity=0.543  Sum_probs=144.8

Q ss_pred             hhhHHhhCcCcccchhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCc
Q psy3653           7 LFFDDHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNT   86 (202)
Q Consensus         7 ~~~~~~~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~   86 (202)
                      +|+-.-.+++|.|+++.+.++.||..||+|..|+..|....|+.+++.        +++++  ..|...|.+++|+++++
T Consensus        16 ~i~c~~c~~kc~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~gevvsa~gk   85 (670)
T KOG1044|consen   16 GIKCDKCRKKCSGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGEVVSTLGK   85 (670)
T ss_pred             ceehhhhCCccccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccceeEecccc
Confidence            344555677889999999999999999999999999999999988886        44555  77888999999999999


Q ss_pred             eecccCCCCCCCCCCCCCCce-eecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCc-ccceeeecCcc
Q psy3653          87 QWHSTCFVCRDCKKPVTGKSF-YAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPI-TGRCITAMFRK  164 (202)
Q Consensus        87 ~~H~~Cf~C~~C~~~l~~~~~-~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I-~~~~~~~~~~~  164 (202)
                      .||++||.|+.|+.|+...+. ...+...+|..+.+......          ........|++|++.| .|+.+.|+++.
T Consensus        86 tyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p----------~~~~~ps~cagc~~~lk~gq~llald~q  155 (670)
T KOG1044|consen   86 TYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSP----------AESYGPSTCAGCGEELKNGQALLALDKQ  155 (670)
T ss_pred             eeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCc----------ccccCCccccchhhhhhccceeeeeccc
Confidence            999999999999999955444 44444566666554433321          1113456799999999 79999999999


Q ss_pred             cccccccccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         165 FHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       165 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      ||..||+|..|...|. ++++.+||.|||..+|.+.||
T Consensus       156 whv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fg  192 (670)
T KOG1044|consen  156 WHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFG  192 (670)
T ss_pred             eeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcC
Confidence            9999999999999997 579999999999999999998

>KOG1703|consensus

Probab=99.93  E-value=1.7e-27  Score=206.58  Aligned_cols=160  Identities=43%  Similarity=0.864  Sum_probs=150.6

Q ss_pred             chhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCceecccCCCCCCCC
Q psy3653          20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCK   99 (202)
Q Consensus        20 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~   99 (202)
                      +.+.++++.||+.+|.|..|+..+....+...||.+||.+|+.+.+.+.|.+|.++|.++.|.|.+..||++||.|..|+
T Consensus       317 ~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~  396 (479)
T KOG1703|consen  317 KVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFVCADCG  396 (479)
T ss_pred             eeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhceeeeccc
Confidence            78889999999999999999999988888999999999999999999999999999999999999999999999999998


Q ss_pred             CCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcc--cceeeecCccccccccccccccc
Q psy3653         100 KPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPIT--GRCITAMFRKFHPEHFVCAFCLR  177 (202)
Q Consensus       100 ~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~--~~~~~~~~~~~H~~Cf~C~~C~~  177 (202)
                      ++|.+..                  ++..++.+||+.+|..++..+|..|.+||.  +..+.+.+..||..||+|+.|.+
T Consensus       397 ~~~~~~~------------------~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~  458 (479)
T KOG1703|consen  397 KPLKNSS------------------FFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMK  458 (479)
T ss_pred             CCCCCCc------------------ccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhc
Confidence            8887754                  456888999999999999999999999985  78899999999999999999999


Q ss_pred             ccCCCceEeeCCcccChhhH
Q psy3653         178 QLNKGTFKEQNDKPYCHGCF  197 (202)
Q Consensus       178 ~l~~~~~~~~~~~~yC~~c~  197 (202)
                      .|.++.|+...++|+|.+|+
T Consensus       459 ~l~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  459 KLTKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             cccCCceeecCCccccccCC
Confidence            99999999999999999875

>KOG1044|consensus

Probab=99.89  E-value=1.5e-24  Score=183.73  Aligned_cols=161  Identities=29%  Similarity=0.642  Sum_probs=138.5

Q ss_pred             ccchhcccccccccccccccccccccCCCcee-eeCCeeecccccccc--------CCCCCcccccccc-cccccccCce
Q psy3653          18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFH-EKDGKPYCRDDYFDL--------FAPKCGGCNRAIM-ENYVSALNTQ   87 (202)
Q Consensus        18 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~g~~yC~~c~~~~--------~~~~C~~C~~~I~-~~~v~~~~~~   87 (202)
                      .++++.++|++||+.||.|++|+.+.....-. .......|+.|-.-.        ....|++|++.|. ++.+.|+++.
T Consensus        76 ~gevvsa~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~q  155 (670)
T KOG1044|consen   76 EGEVVSTLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQ  155 (670)
T ss_pred             cceeEecccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccc
Confidence            46789999999999999999999998765444 444457788876432        2237999999996 7889999999


Q ss_pred             ecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccceeeecCccccc
Q psy3653          88 WHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHP  167 (202)
Q Consensus        88 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~  167 (202)
                      ||..||+|..|...|.+                   .++.++|.|||+++|.+.|+.+|..|.+-|.|.++.|.|++||+
T Consensus       156 whv~cfkc~~c~~vL~g-------------------ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLqag~kh~HP  216 (670)
T KOG1044|consen  156 WHVSCFKCKSCSAVLNG-------------------EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQAGDKHFHP  216 (670)
T ss_pred             eeeeeeehhhhcccccc-------------------eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhhccCcccCc
Confidence            99999999999999977                   46789999999999999999999999999999999999999999


Q ss_pred             ccccccccccccCCCc-eEeeCCcccChhhH
Q psy3653         168 EHFVCAFCLRQLNKGT-FKEQNDKPYCHGCF  197 (202)
Q Consensus       168 ~Cf~C~~C~~~l~~~~-~~~~~~~~yC~~c~  197 (202)
                      .|-+|+.|+..+..|+ .+.....+|=+.|-
T Consensus       217 tCARCsRCgqmF~eGEEMYlQGs~iWHP~C~  247 (670)
T KOG1044|consen  217 TCARCSRCGQMFGEGEEMYLQGSEIWHPDCK  247 (670)
T ss_pred             chhhhhhhccccccchheeeccccccCCccc
Confidence            9999999999999776 77777777766663

>KOG1701|consensus

Probab=99.88  E-value=7.9e-25  Score=179.84  Aligned_cols=117  Identities=33%  Similarity=0.786  Sum_probs=105.6

Q ss_pred             CCCcccccccccc--cccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCC
Q psy3653          67 PKCGGCNRAIMEN--YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGS  144 (202)
Q Consensus        67 ~~C~~C~~~I~~~--~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~  144 (202)
                      .+|++|++.|++.  .+.||++.||..||+|..|.+.|.++.||.                  .|+++||+.+|.. ..+
T Consensus       275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~------------------v~~k~~CE~cyq~-tle  335 (468)
T KOG1701|consen  275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQ------------------VDGKPYCEGCYQD-TLE  335 (468)
T ss_pred             hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccc------------------cCCcccchHHHHH-HHH
Confidence            3999999999854  679999999999999999999999987765                  5666788888865 478


Q ss_pred             CCCCCCCCcccceeeecCcccccccccccccccccCCCceEe-eCCcccChhhHhhhcC
Q psy3653         145 LCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKE-QNDKPYCHGCFEKLFG  202 (202)
Q Consensus       145 ~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~~~~yC~~c~~~~fg  202 (202)
                      +|..|+++|.+++|.|.|+.||+.||+|..|++.|++..|.+ .++++||..+|.++|+
T Consensus       336 kC~~Cg~~I~d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA  394 (468)
T KOG1701|consen  336 KCNKCGEPIMDRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA  394 (468)
T ss_pred             HHhhhhhHHHHHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC
Confidence            999999999999999999999999999999999999999985 5899999999999986

>KOG1703|consensus

Probab=99.85  E-value=2.8e-22  Score=174.00  Aligned_cols=165  Identities=27%  Similarity=0.490  Sum_probs=152.7

Q ss_pred             chhccccccccccccccc-ccccccCCCceeeeCCeeeccccccccCCCCCccccccccc-ccccccCceecccCCCCCC
Q psy3653          20 KCVTALEKTWHTEHFFCA-QCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIME-NYVSALNTQWHSTCFVCRD   97 (202)
Q Consensus        20 ~~~~~~~~~~H~~Cf~C~-~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~   97 (202)
                      ....+....||..-+++. .+...|....++.+.+.+.+..+|...+.+.|..|.+.|.+ +++.++++.||+.+|.|+.
T Consensus       256 p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~  335 (479)
T KOG1703|consen  256 PLVSAPRPASEGLHMKVEKELPLLLVESEALKKLREEEKPAEYHNVTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEV  335 (479)
T ss_pred             cceecccccccccccccccccchhhcccccccccccccccccccccccccccccccCcccceeEeeccccccccceeecc
Confidence            456778999999999999 88888888889999999999999999999999999999998 9999999999999999999


Q ss_pred             CCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccceeeecCccccccccccccccc
Q psy3653          98 CKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLR  177 (202)
Q Consensus        98 C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf~C~~C~~  177 (202)
                      |...+....+                  ...+|.+||..++.+.+++.|.+|+++|.++.|.+.++.||++||.|..|++
T Consensus       336 ~~~~~~~~~~------------------~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~v~a~~~~wH~~cf~C~~C~~  397 (479)
T KOG1703|consen  336 CAIVILDGGP------------------RELDGKILCHECFHAPFRPNCKRCLLPILEEGVCALGRLWHPECFVCADCGK  397 (479)
T ss_pred             ccccccCCCc------------------cccCCCccHHHHHHHhhCccccccCCchHHhHhhhccCeechhceeeecccC
Confidence            9988865433                  4578899999999999999999999999999999999999999999999999


Q ss_pred             ccCCCceEeeCCcccChhhHhhhcC
Q psy3653         178 QLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       178 ~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      +|.++.|+..++.|||..||.++|+
T Consensus       398 ~~~~~~~~~~~~~pyce~~~~~~~~  422 (479)
T KOG1703|consen  398 PLKNSSFFESDGEPYCEDHYKKLFT  422 (479)
T ss_pred             CCCCCcccccCCccchhhhHhhhcc
Confidence            9999999999999999999999874

>KOG4577|consensus

Probab=99.78  E-value=6.1e-21  Score=149.79  Aligned_cols=121  Identities=29%  Similarity=0.776  Sum_probs=104.4

Q ss_pred             cccccCCCCCccccccccccc-ccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccc
Q psy3653          60 DYFDLFAPKCGGCNRAIMENY-VSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHY  138 (202)
Q Consensus        60 c~~~~~~~~C~~C~~~I~~~~-v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~  138 (202)
                      ++.....|+|++|.+.|.+++ +.++++.||..|++|+.|..+|...                   .|.++|..||++++
T Consensus        27 df~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~dr-------------------CFsR~~s~yCkedF   87 (383)
T KOG4577|consen   27 DFSNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADR-------------------CFSREGSVYCKEDF   87 (383)
T ss_pred             cccccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHH-------------------HhhcCCceeehHHH
Confidence            344445689999999999985 4899999999999999999999763                   45789999999999


Q ss_pred             cccCCCCCCCCCCCcccc-ee-eecCcccccccccccccccccCCCc-eE-eeCCcccChhhHhh
Q psy3653         139 HAKRGSLCAGCHKPITGR-CI-TAMFRKFHPEHFVCAFCLRQLNKGT-FK-EQNDKPYCHGCFEK  199 (202)
Q Consensus       139 ~~~~~~~C~~C~~~I~~~-~~-~~~~~~~H~~Cf~C~~C~~~l~~~~-~~-~~~~~~yC~~c~~~  199 (202)
                      .++|+.+|..|+..|... +| .|.+..||..||.|..|+++|.+|+ |+ ..|.++.|+..|+.
T Consensus        88 fKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~  152 (383)
T KOG4577|consen   88 FKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET  152 (383)
T ss_pred             HHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence            999999999999999544 33 5778899999999999999999776 66 56899999999975

>KOG4577|consensus

Probab=99.76  E-value=4.1e-20  Score=145.15  Aligned_cols=97  Identities=32%  Similarity=0.836  Sum_probs=84.3

Q ss_pred             hhcccccccccccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccc-cc-cccCceecccCCCCCCC
Q psy3653          21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMEN-YV-SALNTQWHSTCFVCRDC   98 (202)
Q Consensus        21 ~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~-~v-~~~~~~~H~~Cf~C~~C   98 (202)
                      +++++++.||..|++|++|..+|.+ .++.++|.+||+++|+++|+.+|..|...|.+. +| .|.+..||..||.|..|
T Consensus        48 ilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC  126 (383)
T KOG4577|consen   48 ILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFIC  126 (383)
T ss_pred             HHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhh
Confidence            5789999999999999999999976 477999999999999999999999999999854 44 68899999999999999


Q ss_pred             CCCC-CCCceeecC-CcccCCC
Q psy3653          99 KKPV-TGKSFYAME-GKPDCRQ  118 (202)
Q Consensus        99 ~~~l-~~~~~~~~~-~~~~C~~  118 (202)
                      ++.| ++++||.++ .+..|..
T Consensus       127 ~R~L~TGdEFYLmeD~rLvCK~  148 (383)
T KOG4577|consen  127 KRQLATGDEFYLMEDARLVCKD  148 (383)
T ss_pred             hcccccCCeeEEeccceeehhh
Confidence            9999 788888753 2444433

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.61  E-value=6.5e-16  Score=96.40  Aligned_cols=56  Identities=50%  Similarity=1.025  Sum_probs=51.1

Q ss_pred             CCCCCCCccccee--eecCcccccccccccccccccCCCceEeeCCcccChhhHhhhc
Q psy3653         146 CAGCHKPITGRCI--TAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF  201 (202)
Q Consensus       146 C~~C~~~I~~~~~--~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~f  201 (202)
                      |++|+++|.+..+  .+.|+.||++||+|..|+++|.++.++..+++|||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            7899999964433  5999999999999999999999999999999999999999987

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.37  E-value=2.2e-13  Score=84.87  Aligned_cols=44  Identities=50%  Similarity=1.083  Sum_probs=40.8

Q ss_pred             hcccccccccccccccccccccCCCceeeeCCeeeccccccccC
Q psy3653          22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF   65 (202)
Q Consensus        22 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~   65 (202)
                      +.++|+.||+.||+|+.|+++|.+..++..||++||++||.++|
T Consensus        15 ~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen   15 IKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             EEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             EEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            36999999999999999999999888999999999999998764

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>KOG1700|consensus

Probab=99.25  E-value=2e-12  Score=100.11  Aligned_cols=136  Identities=26%  Similarity=0.542  Sum_probs=100.9

Q ss_pred             CCCCCcccccccc-cccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCC-----Cceee----------c
Q psy3653          65 FAPKCGGCNRAIM-ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG-----GSFFD----------H  128 (202)
Q Consensus        65 ~~~~C~~C~~~I~-~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~-----~~~~~----------~  128 (202)
                      ...+|..|++.+. .+.+...+..||+.||+|..|.+.|...+....++.++|..+...     +..+.          .
T Consensus         6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (200)
T KOG1700|consen    6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK   85 (200)
T ss_pred             ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence            4568999999997 445558899999999999999999998888889999999873210     00000          0


Q ss_pred             CCCcc---cccc-----ccccCCCCCCCCCCCc-ccceeeecCcccccccccccccccccCCCceEeeCCcccChhhHhh
Q psy3653         129 EGLPY---CETH-----YHAKRGSLCAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       129 ~g~~~---C~~~-----~~~~~~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      ++...   ...-     ........|.+|++.+ ..+.+...+..||+.||+|+.|+..|+.+.+...++.+||...+.+
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~  165 (200)
T KOG1700|consen   86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQ  165 (200)
T ss_pred             ccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhhe
Confidence            11110   1000     0111245799999999 5667888899999999999999999999999999999999766654


Q ss_pred             h
Q psy3653         200 L  200 (202)
Q Consensus       200 ~  200 (202)
                      +
T Consensus       166 ~  166 (200)
T KOG1700|consen  166 L  166 (200)
T ss_pred             e
Confidence            3

>KOG1700|consensus

Probab=99.13  E-value=1.4e-11  Score=95.41  Aligned_cols=107  Identities=29%  Similarity=0.684  Sum_probs=85.6

Q ss_pred             hCcCcccch-----hcccccccccccccccccccccCCCceeeeCCeeeccccccccCCC--------------------
Q psy3653          13 FSLRCFQKC-----VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP--------------------   67 (202)
Q Consensus        13 ~~~~C~~~~-----~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~--------------------   67 (202)
                      -|++|.+.+     +...|..||+.||+|..|.+.|+...+.++++.+||+.+|...+++                    
T Consensus         9 kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (200)
T KOG1700|consen    9 KCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGK   88 (200)
T ss_pred             hhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCcccc
Confidence            577885433     3456899999999999999999999999999999999976444332                    


Q ss_pred             ---------------------CCccccccccc-ccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCC
Q psy3653          68 ---------------------KCGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP  119 (202)
Q Consensus        68 ---------------------~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~  119 (202)
                                           .|.+|++.+.+ +.+...+..||..||+|+.|+..|+..++....+.++|..+
T Consensus        89 ~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~  162 (200)
T KOG1700|consen   89 SLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHH  162 (200)
T ss_pred             cccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchh
Confidence                                 29999999984 56678899999999999999999988777665555555443

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=98.80  E-value=3.3e-09  Score=60.17  Aligned_cols=36  Identities=44%  Similarity=0.918  Sum_probs=32.6

Q ss_pred             CCCCCCCCccc--ceeeecCcccccccccccccccccC
Q psy3653         145 LCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLN  180 (202)
Q Consensus       145 ~C~~C~~~I~~--~~~~~~~~~~H~~Cf~C~~C~~~l~  180 (202)
                      +|.+|+++|.+  ..+.+.++.||++||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            58999999965  6788899999999999999999986

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=98.55  E-value=4e-08  Score=55.56  Aligned_cols=36  Identities=42%  Similarity=1.037  Sum_probs=32.0

Q ss_pred             CCccccccccc--ccccccCceecccCCCCCCCCCCCC
Q psy3653          68 KCGGCNRAIME--NYVSALNTQWHSTCFVCRDCKKPVT  103 (202)
Q Consensus        68 ~C~~C~~~I~~--~~v~~~~~~~H~~Cf~C~~C~~~l~  103 (202)
                      +|.+|+++|.+  ..+.+++..||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            58899999986  5778899999999999999999885

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>KOG0490|consensus

Probab=97.48  E-value=2.6e-05  Score=61.67  Aligned_cols=90  Identities=31%  Similarity=0.764  Sum_probs=72.3

Q ss_pred             hhcccccccccccccccccccccC--CCceeeeCCeeeccccccc--cCCCCCcccccccc--cccccccCceecccCCC
Q psy3653          21 CVTALEKTWHTEHFFCAQCGKQFG--EDGFHEKDGKPYCRDDYFD--LFAPKCGGCNRAIM--ENYVSALNTQWHSTCFV   94 (202)
Q Consensus        21 ~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~g~~yC~~c~~~--~~~~~C~~C~~~I~--~~~v~~~~~~~H~~Cf~   94 (202)
                      .+.+.+..||..|++|..|..+|.  ...|.. +|..||..+|..  .+..+|.+|...+.  +.+..+.... |-.||.
T Consensus        11 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~   88 (235)
T KOG0490|consen   11 LLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFA   88 (235)
T ss_pred             HhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccc
Confidence            345568999999999999999997  444445 999999999998  78889999999986  4455566666 999999


Q ss_pred             CCCCCCCC-CCCceeecCC
Q psy3653          95 CRDCKKPV-TGKSFYAMEG  112 (202)
Q Consensus        95 C~~C~~~l-~~~~~~~~~~  112 (202)
                      |..|.+.+ ...++.+..|
T Consensus        89 ~r~~la~~~~~~e~rVqvw  107 (235)
T KOG0490|consen   89 CRECLALLLTGDEFRVQVW  107 (235)
T ss_pred             hHHHHhhcCCCCeeeeehh
Confidence            99998876 5666666555

>KOG0490|consensus

Probab=97.30  E-value=8.1e-05  Score=58.83  Aligned_cols=109  Identities=28%  Similarity=0.579  Sum_probs=82.3

Q ss_pred             cccccccc-cccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCceeecCCCccccccccc--cCCCCCCC
Q psy3653          72 CNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHA--KRGSLCAG  148 (202)
Q Consensus        72 C~~~I~~~-~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~--~~~~~C~~  148 (202)
                      |+..|.+. .+.+.+..||..|..|..|..+|...                 ...+.++|..||..++..  .+..+|.+
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~-----------------~~~~~~~g~~~~~~d~~~~~~~~~rr~r   64 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVG-----------------DTCFSKDGSIYCKRDYQREFKFSKRCAR   64 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccC-----------------CCcccCCCcccccccchhhhhccccccC
Confidence            56677665 34566899999999999999888611                 123345888999999987  67889999


Q ss_pred             CCCCc--ccceeeecCcccccccccccccccccCCCc-eEeeCC-cccChhhHh
Q psy3653         149 CHKPI--TGRCITAMFRKFHPEHFVCAFCLRQLNKGT-FKEQND-KPYCHGCFE  198 (202)
Q Consensus       149 C~~~I--~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~-~~~~~~-~~yC~~c~~  198 (202)
                      |...|  .+++..+..+. |..||.|..|.+.+..++ +.+.+. +..|...+.
T Consensus        65 t~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~  117 (235)
T KOG0490|consen   65 CKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK  117 (235)
T ss_pred             CCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence            99998  35555667777 999999999999876555 666555 777776654

>KOG1702|consensus

Probab=97.07  E-value=5.4e-05  Score=57.78  Aligned_cols=57  Identities=25%  Similarity=0.523  Sum_probs=48.0

Q ss_pred             CCCCCCCCCc-ccceeeecCcccccccccccccccccCCCceEeeCCcccChhhHhhh
Q psy3653         144 SLCAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKL  200 (202)
Q Consensus       144 ~~C~~C~~~I-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~  200 (202)
                      ..|..|++.+ .-+-|.-+++.||..||+|..|+.+|+-..+-..+.+|||...|.+.
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq   62 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQ   62 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccc
Confidence            3466788877 34557888999999999999999999988888889999999998654

>KOG1702|consensus

Probab=96.62  E-value=0.00051  Score=52.54  Aligned_cols=60  Identities=22%  Similarity=0.546  Sum_probs=49.6

Q ss_pred             CCCccccccccc-ccccccCceecccCCCCCCCCCCCCCCceeecCCcccCCCCCCCCcee
Q psy3653          67 PKCGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFF  126 (202)
Q Consensus        67 ~~C~~C~~~I~~-~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~~~~~~~~~  126 (202)
                      +.+..|++.+.+ +-+.-+++.||..||+|..|+.+|.-..+...+.+|+|...++++.+.
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at   65 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT   65 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence            456778888874 567788999999999999999999888888888899998888776554

>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators

Probab=91.59  E-value=0.071  Score=29.58  Aligned_cols=32  Identities=31%  Similarity=0.658  Sum_probs=23.0

Q ss_pred             CCCCCCCcccce--eeecCcccccccccccccccccC
Q psy3653         146 CAGCHKPITGRC--ITAMFRKFHPEHFVCAFCLRQLN  180 (202)
Q Consensus       146 C~~C~~~I~~~~--~~~~~~~~H~~Cf~C~~C~~~l~  180 (202)
                      |.-|+++|.++.  +...++.|+   |.|..|.+.|.
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~fk   34 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQFK   34 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEE---EECHHHHHHHH
Confidence            677999996654  456788888   66677766553

It is thought to function as a metal-sensing regulatory module [].

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=91.03  E-value=0.2  Score=31.36  Aligned_cols=48  Identities=15%  Similarity=0.254  Sum_probs=24.8

Q ss_pred             ccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccc
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV   81 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v   81 (202)
                      ++|+.|..-|...-....=+..||..|..+.++..|..|+.|...+.+
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~qD~   55 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQDI   55 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-SS-
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHHHH
Confidence            678888887766544455567899999999888999999998864433

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.21  E-value=0.33  Score=29.31  Aligned_cols=38  Identities=18%  Similarity=0.433  Sum_probs=26.2

Q ss_pred             CCCCCCCCCCCcc--cceee--ecCcccccccc----cccc--ccccc
Q psy3653         142 RGSLCAGCHKPIT--GRCIT--AMFRKFHPEHF----VCAF--CLRQL  179 (202)
Q Consensus       142 ~~~~C~~C~~~I~--~~~~~--~~~~~~H~~Cf----~C~~--C~~~l  179 (202)
                      .+.+|..|+++|.  +.+|+  .-+..||++|.    .|..  |+..+
T Consensus         4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             cCccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence            3578999999993  34332  34788999997    4665  55543

>KOG2462|consensus

Probab=82.76  E-value=0.81  Score=36.98  Aligned_cols=129  Identities=17%  Similarity=0.351  Sum_probs=74.2

Q ss_pred             cccccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccccccccccCceecccCCCCCCCCCCCCCCceeec
Q psy3653          31 TEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAM  110 (202)
Q Consensus        31 ~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~  110 (202)
                      ...++|.+|++.++...=..+..+.-|.-+-  .-+..|..|++.-.......|-..-|.-=+.|..|++.|...  |..
T Consensus       128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s--~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRP--WLL  203 (279)
T KOG2462|consen  128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDS--KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRP--WLL  203 (279)
T ss_pred             CCceeccccccccccccccchhhcccccccc--cccccCCCCCceeeehHHHhhHhhccCCCcccccccccccch--HHh
Confidence            4568999999998765444566666665544  334589999987653322233344466567899999887531  111


Q ss_pred             CCcccCCCCCCCCceeecCCCccccccccccCCCCCCCCCCCcccce-eeec-CcccccccccccccccccCCCce
Q psy3653         111 EGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRC-ITAM-FRKFHPEHFVCAFCLRQLNKGTF  184 (202)
Q Consensus       111 ~~~~~C~~~~~~~~~~~~~g~~~C~~~~~~~~~~~C~~C~~~I~~~~-~~~~-~~~~H~~Cf~C~~C~~~l~~~~~  184 (202)
                      .|+.           -.+.|         + ..-.|+.|++...++. +.|- ...=+.+=|.|..|++.+....+
T Consensus       204 QGHi-----------RTHTG---------E-KPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~Sy  258 (279)
T KOG2462|consen  204 QGHI-----------RTHTG---------E-KPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALKSY  258 (279)
T ss_pred             hccc-----------ccccC---------C-CCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHHHH
Confidence            1110           00000         0 1235889998886642 2221 11123335788999888775443

>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=82.29  E-value=0.46  Score=26.04  Aligned_cols=32  Identities=16%  Similarity=0.625  Sum_probs=22.6

Q ss_pred             hCcCcccchhcccccccccccccccccccccC
Q psy3653          13 FSLRCFQKCVTALEKTWHTEHFFCAQCGKQFG   44 (202)
Q Consensus        13 ~~~~C~~~~~~~~~~~~H~~Cf~C~~C~~~l~   44 (202)
                      .|+.|..++....++.||..=..|..||=+++
T Consensus         1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~~   32 (35)
T PF07503_consen    1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRYS   32 (35)
T ss_dssp             --HHHHHHHCSTTSTTTT-TT--BTTCC-SCC
T ss_pred             CCHHHHHHHcCCCCCcccCcCccCCCCCCCEE
Confidence            37778888888899999999999999987663

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=81.13  E-value=1.2  Score=25.36  Aligned_cols=28  Identities=36%  Similarity=0.822  Sum_probs=19.4

Q ss_pred             cccccccccccccccCCCceeeeCCeeecccc
Q psy3653          29 WHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDD   60 (202)
Q Consensus        29 ~H~~Cf~C~~C~~~l~~~~~~~~~g~~yC~~c   60 (202)
                      |-.-=-.|..|+.||-    ..++|+.||..|
T Consensus        13 ~~ML~~~Cp~C~~PL~----~~k~g~~~Cv~C   40 (41)
T PF06677_consen   13 WTMLDEHCPDCGTPLM----RDKDGKIYCVSC   40 (41)
T ss_pred             HhHhcCccCCCCCeeE----EecCCCEECCCC
Confidence            4444446778888873    368999998765

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[]

Probab=81.12  E-value=1.2  Score=24.58  Aligned_cols=25  Identities=32%  Similarity=0.535  Sum_probs=18.9

Q ss_pred             ccccccccccCCCceeeeCCeeecccccc
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYF   62 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~   62 (202)
                      +.|..|+..    .|...||..||..|-.
T Consensus         9 ~~C~~C~~~----~~~~~dG~~yC~~cG~   33 (36)
T PF11781_consen    9 EPCPVCGSR----WFYSDDGFYYCDRCGH   33 (36)
T ss_pred             CcCCCCCCe----EeEccCCEEEhhhCce
Confidence            347888765    4778999999987754

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	202
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		2e-16
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		3e-05
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		4e-08
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		8e-07
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		2e-07
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		1e-06
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		3e-07
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		8e-07
1nyp_A	66	4th Lim Domain Of Pinch Protein Length = 66		5e-07
1nyp_A	66	4th Lim Domain Of Pinch Protein Length = 66		4e-06
2xqn_T	126	Complex Of The 2nd And 3rd Lim Domains Of Tes With		6e-07
2xqn_T	126	Complex Of The 2nd And 3rd Lim Domains Of Tes With		1e-04
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		2e-06
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		2e-06
2dar_A	90	Solution Structure Of First Lim Domain Of Enigma-Li		3e-06
2cuq_A	80	Solution Structure Of Second Lim Domain From Human		1e-05
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		2e-05
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		5e-05
2d8z_A	70	Solution Structure Of The Third Lim Domain Of Four		1e-04
1g47_A	77	1st Lim Domain Of Pinch Protein Length = 77		1e-04
2kbx_B	70	Solution Structure Of Ilk-Pinch Complex Length = 70		1e-04
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		3e-04
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		3e-04
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		3e-04
2cur_A	69	Solution Structure Of Skeletal Muscle Lim-Protein 1		4e-04
2cup_A	101	Solution Structure Of The Skeletal Muscle Lim-Prote		8e-04

>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin Length = 80

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/85 (45%), Positives = 51/85 (60%), Gaps = 18/85 (21%)
Query: 60  DYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119
           D+  +F+PKCGGCNR ++ENY+SA++T WH  CFVC                   DC   
Sbjct: 9   DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCG------------------DCFTS 50
Query: 120 FQGGSFFDHEGLPYCETHYHAKRGS 144
           F  GSFF+ +G P+CE HYH +RGS
Sbjct: 51  FSTGSFFELDGRPFCELHYHHRRGS 75

>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin Length = 80

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 18/48 (37%), Positives = 29/48 (60%)
Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC 193
           C GC++P+    ++AM   +HPE FVC  C    + G+F E + +P+C
Sbjct: 18  CGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFC 65

>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of Transcription Factors, The Lim-Homeodomain Proteins, In Neural Cell Type Specification Length = 169

Iteration: 1
 Score = 54.7 bits (130), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/104 (31%), Positives = 52/104 (50%), Gaps = 5/104 (4%)
Query: 22  VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV 81
           +  L++ WH+    CA C  Q  +  F  + G  YC++D+F  F  KC  C + I    V
Sbjct: 22  LKVLDRHWHSSCLKCADCQMQLADRCF-SRAGSVYCKEDFFKRFGTKCTACQQGIPPTQV 80
Query: 82  --SALNTQWHSTCFVCRDCKKPV-TGKSFYAME-GKPDCRQPFQ 121
              A +  +H  CF C  C + + TG  FY ME G+  C++ ++
Sbjct: 81  VRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKEDYE 124

>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of Transcription Factors, The Lim-Homeodomain Proteins, In Neural Cell Type Specification Length = 169

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 31/119 (26%), Positives = 49/119 (41%), Gaps = 22/119 (18%)
Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           P+C GCN+ I++ ++   L+  WHS+C  C DC+  +  +                    
Sbjct: 7   PQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRC------------------- 47
Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF--HPEHFVCAFCLRQLNKG 182
           F   G  YC+  +  + G+ C  C + I    +    + F  H   F C  C RQL  G
Sbjct: 48  FSRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATG 106

>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The Binding Domain Of Isl1 Length = 169

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 22  VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV 81
           + AL++ WH++   C+ C     E  F   +   YC+DD+F  F  KC  C   I    V
Sbjct: 22  LKALDRHWHSKCLKCSDCHVPLAERCFSRGESV-YCKDDFFKRFGTKCAACQLGIPPTQV 80
Query: 82  --SALNTQWHSTCFVCRDCKKPV-TGKSFYAME 111
              A +  +H  CF C  CK+ + TG  FY ME
Sbjct: 81  VRRAQDFVYHLHCFACVVCKRQLATGDEFYLME 113

>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The Binding Domain Of Isl1 Length = 169

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 48/119 (40%), Gaps = 22/119 (18%)
Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           P C GC++ I++ ++  AL+  WHS C  C DC  P+  + F   E              
Sbjct: 7   PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESV------------ 54
Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF--HPEHFVCAFCLRQLNKG 182
                  YC+  +  + G+ CA C   I    +    + F  H   F C  C RQL  G
Sbjct: 55  -------YCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATG 106

>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex Length = 182

Iteration: 1
 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 45/93 (48%), Gaps = 4/93 (4%)
Query: 22  VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV 81
           + AL++ WH++   C+ C     E  F   +   YC+DD+F  F  KC  C   I    V
Sbjct: 76  LKALDRHWHSKCLKCSDCHVPLAERCFSRGESV-YCKDDFFKRFGTKCAACQLGIPPTQV 134
Query: 82  --SALNTQWHSTCFVCRDCKKPV-TGKSFYAME 111
              A +  +H  CF C  CK+ + TG  FY ME
Sbjct: 135 VRRAQDFVYHLHCFACVVCKRQLATGDEFYLME 167

>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex Length = 182

Iteration: 1
 Score = 50.1 bits (118), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 48/119 (40%), Gaps = 22/119 (18%)
Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           P C GC++ I++ ++  AL+  WHS C  C DC  P+  + F   E              
Sbjct: 61  PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGES------------- 107
Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF--HPEHFVCAFCLRQLNKG 182
                  YC+  +  + G+ CA C   I    +    + F  H   F C  C RQL  G
Sbjct: 108 ------VYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATG 160

>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein Length = 66

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 37/83 (44%), Gaps = 18/83 (21%)
Query: 63  DLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
            +  P CG C R I    V+A+  QWH   FVC  C+K                  PF G
Sbjct: 2   SMGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEK------------------PFLG 43
Query: 123 GSFFDHEGLPYCETHYHAKRGSL 145
              ++ +GL YCETHY+   G +
Sbjct: 44  HRHYERKGLAYCETHYNQLFGDV 66

>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein Length = 66

Iteration: 1
 Score = 47.8 bits (112), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 22/58 (37%), Positives = 32/58 (55%)
Query: 145 LCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           +C  C +PI GR + AM +++H EHFVCA C +        E+    YC   + +LFG
Sbjct: 7   ICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 64

>pdb|2XQN|T Chain T, Complex Of The 2nd And 3rd Lim Domains Of Tes With The Evh1 Domain Of Mena And The N-Terminal Domain Of Actin-Like Protein Arp7a Length = 126

Iteration: 1
 Score = 50.4 bits (119), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 30/93 (32%), Positives = 44/93 (47%), Gaps = 4/93 (4%)
Query: 24  ALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENY--V 81
           A  + WH +HF C  C      + +   + KP C+  Y    A  C GC+ AI      V
Sbjct: 21  AENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRV 80
Query: 82  SALNTQWHST--CFVCRDCKKPVTGKSFYAMEG 112
           +  N  WH++  CF+C  C K + G+ F  +EG
Sbjct: 81  TYNNFSWHASTECFLCSCCSKCLIGQKFMPVEG 113

>pdb|2XQN|T Chain T, Complex Of The 2nd And 3rd Lim Domains Of Tes With The Evh1 Domain Of Mena And The N-Terminal Domain Of Actin-Like Protein Arp7a Length = 126

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/132 (26%), Positives = 48/132 (36%), Gaps = 23/132 (17%)
Query: 67  PKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           P+C GC+  I  N Y  A N  WH   F C DC   + G+ +  +  KP C+        
Sbjct: 4   PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKP------- 56
Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKF----HPEHFVCAFCLRQLNK 181
                   C    HA    +C GCH  I        +  F      E F+C+ C + L  
Sbjct: 57  --------CYVKNHA---VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIG 105
Query: 182 GTFKEQNDKPYC 193
             F       +C
Sbjct: 106 QKFMPVEGMVFC 117

>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim Domains 1 And 2 With The Lim Interacting Domain Of Ldb1 Length = 195

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/100 (31%), Positives = 47/100 (47%), Gaps = 7/100 (7%)
Query: 24  ALEKTWHTEHFFCAQCGKQFGEDGF--HEKDGKPYCRDDYFDLF--APKCGGCNRAI--M 77
           A++  WH+    C+ C  Q G+ G   + K G   CR+DY  LF  +  C  C ++I   
Sbjct: 21  AMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPAS 80
Query: 78  ENYVSALNTQWHSTCFVCRDCK-KPVTGKSFYAMEGKPDC 116
           E  + A    +H  CF C  C+ + V G  F+ + G   C
Sbjct: 81  ELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFC 120

>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid Domain Length = 188

Iteration: 1
 Score = 48.5 bits (114), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/100 (31%), Positives = 47/100 (47%), Gaps = 7/100 (7%)
Query: 24  ALEKTWHTEHFFCAQCGKQFGEDGF--HEKDGKPYCRDDYFDLF--APKCGGCNRAI--M 77
           A++  WH+    C+ C  Q G+ G   + K G   CR+DY  LF  +  C  C ++I   
Sbjct: 23  AMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPAS 82
Query: 78  ENYVSALNTQWHSTCFVCRDCK-KPVTGKSFYAMEGKPDC 116
           E  + A    +H  CF C  C+ + V G  F+ + G   C
Sbjct: 83  ELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFC 122

>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like Pdz And Lim Domains Protein Length = 90

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/80 (36%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 123 GSFFDHEGLPYCETHYHA-KRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNK 181
           GS  D + L     H  A KR  +CA C++ I G  + A+ + +HPE F CA C   +  
Sbjct: 4   GSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAY 63
Query: 182 GTFKEQNDKPYCHGCFEKLF 201
             F E+    YC  C+EK F
Sbjct: 64  IGFVEEKGALYCELCYEKFF 83

>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human Skeletal Muscle Lim-Protein 2 Length = 80

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 31/56 (55%)
Query: 61  YFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDC 116
           Y + FAP+C  C++ + +  V+  +  WH  C VC  C+ P+ G+ F + +  P C
Sbjct: 10  YENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYC 65

>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21 Crystal Form Length = 131

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/106 (28%), Positives = 46/106 (43%), Gaps = 7/106 (6%)
Query: 22  VTALEKTWHTEHFFCAQCGKQFGEDG--FHEKDGKPYCRDDYFDLFAPK--CGGCNRAIM 77
           + A+++ WH +   C  CG + GE G   + K G+  CR DY  LF     C  C++ I 
Sbjct: 18  LKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIR 77
Query: 78  --ENYVSALNTQWHSTCFVCRDCKKP-VTGKSFYAMEGKPDCRQPF 120
             E  +   +  +H  CF C  C+K    G  +  +     C Q  
Sbjct: 78  AYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI 123

>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim Protein 3 Length = 80

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 25/77 (32%), Positives = 36/77 (46%), Gaps = 20/77 (25%)
Query: 69  CGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFD 127
           C GC   I     + AL+ QWH +CF C+ C   +TG+                   +  
Sbjct: 18  CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGE-------------------YIS 58
Query: 128 HEGLPYCETHYHAKRGS 144
            +G+PYCE+ YHA+ GS
Sbjct: 59  KDGVPYCESDYHAQFGS 75

>pdb|2D8Z|A Chain A, Solution Structure Of The Third Lim Domain Of Four And A Half Lim Domains Protein 2 (Fhl-2) Length = 70

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 31/58 (53%)
Query: 144 SLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           S C  C KPIT   +T   + +H E FVC  C +QL+   F  ++D  YC  CF  L+
Sbjct: 6   SGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY 63

>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein Length = 77

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP 67
          +K V +  + +H + F CAQC +QF E  F+E +G+ YC  D+  LFAP
Sbjct: 25 EKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP 73

>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex Length = 70

Iteration: 1
 Score = 42.7 bits (99), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 31/49 (63%)
Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP 67
          +K V +  + +H + F CAQC +QF E  F+E +G+ YC  D+  LFAP
Sbjct: 21 EKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP 69

>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The Cysteine Rich Protein Crp Length = 85

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 24/47 (51%)
Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPK 68
          V    K+WH   F CA+CGK        +KDG+ YC+  Y   F PK
Sbjct: 24 VIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 70

>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1 Length = 192

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/47 (40%), Positives = 24/47 (51%)
Query: 22  VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPK 68
           V    K+WH   F CA+CGK        +KDG+ YC+  Y   F PK
Sbjct: 131 VIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures Length = 76

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDD-YFDLFAPKCGGCNRAI 76
          F + VT+L K WH     C +CGK     G  E +GKPYC    Y  +F PK  G  R  
Sbjct: 12 FAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPK--GFGRGG 69
Query: 77 MENYV 81
           E++ 
Sbjct: 70 AESHT 74

>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1 Length = 69

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 69  CGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGK---PDCRQPFQGG 123
           C  CN+AI    ++  +  WH+ CFVC  C K + G+ F A+E +    DC + F  G
Sbjct: 8   CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSG 65

>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1 Length = 101

Iteration: 1
 Score = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 29 WHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM--ENYVSALNT 86
          WH   F CA+C      + F  KD K  C        +PKC GC +AI+  +  V    T
Sbjct: 29 WHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGT 88
Query: 87 QWHSTCF 93
           WH  CF
Sbjct: 89 VWHKDCF 95

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	202
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	7e-38
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-27
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	9e-20
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	6e-10
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-34
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	4e-27
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-15
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-08
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-31
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-28
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-11
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-07
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-27
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-24
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-27
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-19
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	5e-12
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	4e-27
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	1e-17
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-16
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	6e-27
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-26
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-09
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	4e-08
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	7e-27
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-20
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-11
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	7e-26
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	4e-22
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	6e-16
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-21
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-20
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-17
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	4e-21
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-16
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	2e-13
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	8e-20
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	3e-16
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	8e-15
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-19
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-16
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	2e-15
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-18
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	9e-17
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	1e-18
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	4e-18
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	4e-16
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	3e-18
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	3e-15
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	9e-15
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	7e-18
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	3e-16
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	7e-15
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	1e-17
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-13
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	8e-13
2cor_A	79	Pinch protein; LIM domain, particularly interestin	4e-17
2cor_A	79	Pinch protein; LIM domain, particularly interestin	5e-10
2cor_A	79	Pinch protein; LIM domain, particularly interestin	2e-06
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	7e-17
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	2e-16
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	2e-09
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	1e-16
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-16
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	6e-16
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-16
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	1e-13
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	1e-12
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-16
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	1e-14
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	9e-13
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	7e-16
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	9e-16
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	4e-08
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-15
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-12
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-11
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-14
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	3e-11
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-08
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	3e-14
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	5e-14
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	6e-13
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	5e-14
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	1e-13
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	5e-14
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-13
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-12
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	7e-14
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	9e-14
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	3e-12
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-13
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-12
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-12
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	3e-13
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-11
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-11
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-13
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-13
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-12
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	6e-13
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	7e-12
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	8e-10
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	6e-13
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	6e-12
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	6e-12
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-11
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	4e-11
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	3e-11
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	2e-09
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	2e-08
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	6e-10
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	5e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-07
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-09
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	4e-09
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	3e-07
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	7e-08
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	2e-05
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	6e-04
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	9e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	3e-05
2co8_A	82	NEDD9 interacting protein with calponin homology a	8e-05
2co8_A	82	NEDD9 interacting protein with calponin homology a	9e-05

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score =  128 bits (322), Expect = 7e-38
 Identities = 31/156 (19%), Positives = 53/156 (33%), Gaps = 19/156 (12%)

Query: 19  QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM- 77
           +  + AL++ WH++   C+ C     E  F  +    YC+DD+F  F  KC  C   I  
Sbjct: 19  RFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGIPP 77

Query: 78  -ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCET 136
            +    A +  +H  CF C  CK+ +     +                +   +    C+ 
Sbjct: 78  TQVVRRAQDFVYHLHCFACVVCKRQLATGDEF----------------YLMEDSRLVCKA 121

Query: 137 HYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVC 172
            Y   +     G      G  + A   + H      
Sbjct: 122 DYETAKQGGSGGSGGSGGGTPMVAASPERHDGGLQA 157

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score =  101 bits (252), Expect = 2e-27
 Identities = 35/141 (24%), Positives = 53/141 (37%), Gaps = 24/141 (17%)

Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           P C GC++ I++ ++  AL+  WHS C  C DC  P+                       
Sbjct: 7   PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPL-------------------AERC 47

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHK--PITGRCITAMFRKFHPEHFVCAFCLRQLNKGT 183
           F      YC+  +  + G+ CA C    P T     A    +H   F C  C RQL  G 
Sbjct: 48  FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGD 107

Query: 184 --FKEQNDKPYCHGCFEKLFG 202
             +  ++ +  C   +E    
Sbjct: 108 EFYLMEDSRLVCKADYETAKQ 128

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 81.0 bits (200), Expect = 9e-20
 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 2/92 (2%)

Query: 12  HFSLRCFQKCVTALEKTWHTEHFFCAQCGKQF--GEDGFHEKDGKPYCRDDYFDLFAPKC 69
              +   Q    A +  +H   F C  C +Q   G++ +  +D +  C+ DY        
Sbjct: 72  QLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGGS 131

Query: 70  GGCNRAIMENYVSALNTQWHSTCFVCRDCKKP 101
           GG   +     + A + + H         +  
Sbjct: 132 GGSGGSGGGTPMVAASPERHDGGLQANPVEVQ 163

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 54.8 bits (132), Expect = 6e-10
 Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 142 RGSLCAGCHKPITGRCI-TAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKL 200
              +CAGC + I  R I  A+ R +H +   C+ C   L       + +  YC   F K 
Sbjct: 5   EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA-ERCFSRGESVYCKDDFFKR 63

Query: 201 FG 202
           FG
Sbjct: 64  FG 65

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score =  118 bits (298), Expect = 3e-34
 Identities = 37/169 (21%), Positives = 60/169 (35%), Gaps = 24/169 (14%)

Query: 36  CAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENYV-SALNTQWHSTCFV 94
             +  +    +G  ++ G             P C GC++ I++ ++  AL+  WHS C  
Sbjct: 30  RLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLK 89

Query: 95  CRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPI- 153
           C DC  P+                       F      YC+  +  + G+ CA C   I 
Sbjct: 90  CSDCHVPL-------------------AERCFSRGESVYCKDDFFKRFGTKCAACQLGIP 130

Query: 154 -TGRCITAMFRKFHPEHFVCAFCLRQLNKGT--FKEQNDKPYCHGCFEK 199
            T     A    +H   F C  C RQL  G   +  ++ +  C   +E 
Sbjct: 131 PTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 179

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score =  100 bits (251), Expect = 4e-27
 Identities = 33/127 (25%), Positives = 50/127 (39%), Gaps = 21/127 (16%)

Query: 19  QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM- 77
           +  + AL++ WH++   C+ C     E  F  +    YC+DD+F  F  KC  C   I  
Sbjct: 73  RFILKALDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGTKCAACQLGIPP 131

Query: 78  -ENYVSALNTQWHSTCFVCRDCKKP-VTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCE 135
            +    A +  +H  CF C  CK+   TG  FY ME                 +    C+
Sbjct: 132 TQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLME-----------------DSRLVCK 174

Query: 136 THYHAKR 142
             Y   +
Sbjct: 175 ADYETAK 181

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score = 70.3 bits (172), Expect = 2e-15
 Identities = 23/101 (22%), Positives = 34/101 (33%), Gaps = 2/101 (1%)

Query: 103 TGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCI-TAM 161
            G     +  + +  Q        D  G              +CAGC + I  R I  A+
Sbjct: 20  FGDEDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKAL 79

Query: 162 FRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
            R +H +   C+ C   L       + +  YC   F K FG
Sbjct: 80  DRHWHSKCLKCSDCHVPLA-ERCFSRGESVYCKDDFFKRFG 119

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score = 50.3 bits (120), Expect = 3e-08
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 12  HFSLRCFQKCVTALEKTWHTEHFFCAQCGKQF--GEDGFHEKDGKPYCRDDY 61
              +   Q    A +  +H   F C  C +Q   G++ +  +D +  C+ DY
Sbjct: 126 QLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score =  109 bits (275), Expect = 2e-31
 Identities = 31/102 (30%), Positives = 45/102 (44%), Gaps = 4/102 (3%)

Query: 21  CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIMENY 80
              A  + WH +HF C  C      + +   + KP C+  Y    A  C GC+ AI    
Sbjct: 18  YTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEV 77

Query: 81  --VSALNTQWHST--CFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
             V+  N  WH++  CF+C  C K + G+ F  +EG   C  
Sbjct: 78  QRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSV 119

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score =  102 bits (255), Expect = 2e-28
 Identities = 34/140 (24%), Positives = 48/140 (34%), Gaps = 23/140 (16%)

Query: 67  PKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           P+C GC+  I  N Y  A N  WH   F C DC   + G+ +                  
Sbjct: 4   PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVM---------------- 47

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRC--ITAMFRKFHP--EHFVCAFCLRQLNK 181
                 P C+  Y      +C GCH  I      +T     +H   E F+C+ C + L  
Sbjct: 48  --VNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIG 105

Query: 182 GTFKEQNDKPYCHGCFEKLF 201
             F       +C    +K  
Sbjct: 106 QKFMPVEGMVFCSVECKKRM 125

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 58.6 bits (142), Expect = 1e-11
 Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 146 CAGCHKPITGR-CITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           CAGC + I       A  + +H +HF C  C   L    +   NDKP C  C+ K   
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHA 63

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 47.8 bits (114), Expect = 1e-07
 Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 11/69 (15%)

Query: 9   FDDHFSLRCF---------QKCVTALEKTWH--TEHFFCAQCGKQFGEDGFHEKDGKPYC 57
           +  + ++ C           + VT    +WH  TE F C+ C K      F   +G  +C
Sbjct: 58  YVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFC 117

Query: 58  RDDYFDLFA 66
             +     +
Sbjct: 118 SVECKKRMS 126

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score =  101 bits (253), Expect = 2e-27
 Identities = 34/166 (20%), Positives = 53/166 (31%), Gaps = 24/166 (14%)

Query: 19  QKCVTALEKTWHTEHFFCAQCGKQFGEDG--FHEKDGKPYCRDDYFDLF--APKCGGCNR 74
           +  + A++  WH+    C+ C  Q G+ G   + K G   CR+DY  LF  +  C  C +
Sbjct: 18  RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQ 77

Query: 75  AI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLP 132
           +I   E  + A    +H  CF C  C+  +                   G  F    G  
Sbjct: 78  SIPASELVMRAQGNVYHLKCFTCSTCRNRLV-----------------PGDRFHYINGSL 120

Query: 133 YCETHYHAKRGSLCAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLR 177
           +CE        +           G     +     P      F   
Sbjct: 121 FCEHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDE 166

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B Length = 188

 Score = 94.3 bits (234), Expect = 2e-24
 Identities = 31/145 (21%), Positives = 50/145 (34%), Gaps = 22/145 (15%)

Query: 64  LFAPKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
           L   +C GC   I + ++  A+++ WHS C  C  C+  +                   G
Sbjct: 3   LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGD----------------IG 46

Query: 123 GSFFDHEGLPYCETHYHAKRG--SLCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQ 178
            S +   G+  C   Y    G    C+ C + I      + A    +H + F C+ C  +
Sbjct: 47  TSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNR 106

Query: 179 LNKG-TFKEQNDKPYCHGCFEKLFG 202
           L  G  F   N   +C         
Sbjct: 107 LVPGDRFHYINGSLFCEHDRPTALI 131

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score =  101 bits (252), Expect = 3e-27
 Identities = 30/186 (16%), Positives = 50/186 (26%), Gaps = 30/186 (16%)

Query: 18  FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM 77
           F + V     ++H   F C  C K            + YC+  Y   + PK  G      
Sbjct: 19  FAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAG 78

Query: 78  ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLPYCETH 137
                                            +        ++ G              
Sbjct: 79  TLS-----------------------------TDKGESLGIKYEEGQSHRPTNPNASRMA 109

Query: 138 YHAKRGSLCAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
                   C  C + +     +    + +H   F CA C + L   T  +++ + YC GC
Sbjct: 110 QKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGC 169

Query: 197 FEKLFG 202
           + K FG
Sbjct: 170 YAKNFG 175

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 80.8 bits (199), Expect = 2e-19
 Identities = 23/140 (16%), Positives = 35/140 (25%), Gaps = 19/140 (13%)

Query: 11  DHFSLRCFQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCG 70
             +  +   K                   G ++ E   H        R       +  C 
Sbjct: 60  SCYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCP 119

Query: 71  GCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHE 129
            C +A+     V      WH +CF C  C K                    +  +  D +
Sbjct: 120 RCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKS------------------LESTTLADKD 161

Query: 130 GLPYCETHYHAKRGSLCAGC 149
           G  YC+  Y    G    G 
Sbjct: 162 GEIYCKGCYAKNFGPKGFGF 181

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 61.2 bits (148), Expect = 5e-12
 Identities = 20/56 (35%), Positives = 26/56 (46%)

Query: 21  CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAI 76
            V    K+WH   F CA+CGK        +KDG+ YC+  Y   F PK  G  +  
Sbjct: 130 KVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA 185

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 90

 Score = 97.9 bits (244), Expect = 4e-27
 Identities = 29/81 (35%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 123 GSFFDHEGLPYCETHYHA-KRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNK 181
           GS  D + L     H  A KR  +CA C++ I G  + A+ + +HPE F CA C   +  
Sbjct: 4   GSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKNTMAY 63

Query: 182 GTFKEQNDKPYCHGCFEKLFG 202
             F E+    YC  C+EK F 
Sbjct: 64  IGFVEEKGALYCELCYEKFFA 84

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 90

 Score = 73.6 bits (181), Expect = 1e-17
 Identities = 21/101 (20%), Positives = 30/101 (29%), Gaps = 19/101 (18%)

Query: 48  FHEKDGKPYCRDDYFD-LFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKS 106
             ++D      +        P C  CN+ I   ++ AL   WH   F C  CK       
Sbjct: 6   SGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFLVALGKSWHPEEFNCAHCKN------ 59

Query: 107 FYAMEGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCA 147
                             F + +G  YCE  Y     S  +
Sbjct: 60  ------------TMAYIGFVEEKGALYCELCYEKFFASGPS 88

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 90

 Score = 69.4 bits (170), Expect = 3e-16
 Identities = 19/50 (38%), Positives = 22/50 (44%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
            + AL K+WH E F CA C       GF E+ G  YC   Y   FA   
Sbjct: 38 PFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGP 87

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 98.7 bits (246), Expect = 6e-27
 Identities = 32/140 (22%), Positives = 44/140 (31%), Gaps = 22/140 (15%)

Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
             CGGC + I + Y   A++  WH  C  C  C   +                   G   
Sbjct: 3   LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEV----------------GRRL 46

Query: 126 FDHEGLPYCETHYHAKRG--SLCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNK 181
           +   G   C   Y    G   LCA C K I      +    + +H E F CA C +    
Sbjct: 47  YYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCV 106

Query: 182 G-TFKEQNDKPYCHGCFEKL 200
           G  +   N    C     + 
Sbjct: 107 GDRYLLINSDIVCEQDIYEW 126

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 97.5 bits (243), Expect = 2e-26
 Identities = 30/127 (23%), Positives = 47/127 (37%), Gaps = 23/127 (18%)

Query: 19  QKCVTALEKTWHTEHFFCAQCGKQFGEDG--FHEKDGKPYCRDDYFDLFAPK--CGGCNR 74
           +  + A+++ WH +   C  CG + GE G   + K G+  CR DY  LF     C  C++
Sbjct: 15  RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDK 74

Query: 75  AI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFFDHEGLP 132
            I   E  +   +  +H  CF C  C+K                     G  +       
Sbjct: 75  RIRAYEMTMRVKDKVYHLECFKCAACQKHFC-----------------VGDRYLLINSDI 117

Query: 133 YCETHYH 139
            CE   +
Sbjct: 118 VCEQDIY 124

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 52.4 bits (126), Expect = 2e-09
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 145 LCAGCHKPITGR-CITAMFRKFHPEHFVCAFCLRQLNKG--TFKEQNDKPYCHGCFEKLF 201
            C GC + I  R  + A+ + +H +   C  C  +L +       +  +  C   + +LF
Sbjct: 4   TCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLF 63

Query: 202 G 202
           G
Sbjct: 64  G 64

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 49.0 bits (117), Expect = 4e-08
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 19  QKCVTALEKTWHTEHFFCAQCGKQFGE-DGFHEKDGKPYCRDDYFDL 64
           +  +   +K +H E F CA C K F   D +   +    C  D ++ 
Sbjct: 80  EMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEW 126

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 97.5 bits (243), Expect = 7e-27
 Identities = 26/82 (31%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 19  QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM- 77
            K V    + WH   F CA+C      + F  KD K  C        +PKC GC +AI+ 
Sbjct: 19  SKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVA 78

Query: 78  -ENYVSALNTQWHSTCFVCRDC 98
            +  V    T WH  CF     
Sbjct: 79  GDQNVEYKGTVWHKDCFSGPSS 100

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 81.3 bits (201), Expect = 1e-20
 Identities = 22/115 (19%), Positives = 31/115 (26%), Gaps = 22/115 (19%)

Query: 65  FAPKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
            +  C  C + I      V   N  WH TCF C  C  P                     
Sbjct: 4   GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHP------------------LAN 45

Query: 123 GSFFDHEGLPYCETHYHAKRGSLCAGCHKPITG--RCITAMFRKFHPEHFVCAFC 175
            +F   +    C      +    C GC K I    + +      +H + F     
Sbjct: 46  ETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 57.8 bits (140), Expect = 1e-11
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 140 AKRGSLCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           +   S C  C KPI    + +    R +H   F CA CL  L   TF  +++K  C+ C 
Sbjct: 2   SSGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCT 61

Query: 198 EKLFG 202
            +   
Sbjct: 62  TREDS 66

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 94.3 bits (235), Expect = 7e-26
 Identities = 39/95 (41%), Positives = 52/95 (54%), Gaps = 18/95 (18%)

Query: 53  GKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEG 112
                  D+  +F+PKCGGCNR ++ENY+SA++T WH  CFVC DC              
Sbjct: 2   SSGSSGKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFT------------ 49

Query: 113 KPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCA 147
                  F  GSFF+ +G P+CE HYH +RGS  +
Sbjct: 50  ------SFSTGSFFELDGRPFCELHYHHRRGSGPS 78

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 84.7 bits (210), Expect = 4e-22
 Identities = 20/73 (27%), Positives = 33/73 (45%)

Query: 130 GLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQND 189
                   + A     C GC++P+    ++AM   +HPE FVC  C    + G+F E + 
Sbjct: 2   SSGSSGKDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDG 61

Query: 190 KPYCHGCFEKLFG 202
           +P+C   +    G
Sbjct: 62  RPFCELHYHHRRG 74

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 68.5 bits (168), Expect = 6e-16
 Identities = 19/69 (27%), Positives = 26/69 (37%), Gaps = 7/69 (10%)

Query: 9  FDDHFSLRCFQ-------KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          F   FS +C           ++A++  WH E F C  C   F    F E DG+P+C   Y
Sbjct: 10 FLAMFSPKCGGCNRPVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHY 69

Query: 62 FDLFAPKCG 70
                   
Sbjct: 70 HHRRGSGPS 78

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 82.4 bits (204), Expect = 4e-21
 Identities = 22/71 (30%), Positives = 30/71 (42%)

Query: 132 PYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKP 191
                 Y  K    CA C K +T   +T   + +H E  VC  C   L    F  +++ P
Sbjct: 4   GSSGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDP 63

Query: 192 YCHGCFEKLFG 202
           YC  CF +LF 
Sbjct: 64  YCVACFGELFA 74

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 79.3 bits (196), Expect = 4e-20
 Identities = 20/95 (21%), Positives = 32/95 (33%), Gaps = 18/95 (18%)

Query: 53  GKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEG 112
                   Y + FAP+C  C++ + +  V+  +  WH  C VC  C+             
Sbjct: 2   SSGSSGPCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQT------------ 49

Query: 113 KPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCA 147
                 P  G  F   +  PYC   +     S  +
Sbjct: 50  ------PLAGQQFTSRDEDPYCVACFGELFASGPS 78

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 72.7 bits (179), Expect = 2e-17
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 7/68 (10%)

Query: 9  FDDHFSLRC-------FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDY 61
          +++ F+ RC        Q  VT  ++ WH E   C  C        F  +D  PYC   +
Sbjct: 10 YENKFAPRCARCSKTLTQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACF 69

Query: 62 FDLFAPKC 69
           +LFA   
Sbjct: 70 GELFASGP 77

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 82.0 bits (203), Expect = 4e-21
 Identities = 25/97 (25%), Positives = 33/97 (34%), Gaps = 20/97 (20%)

Query: 53  GKPYCRDDYFDLFAPKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAM 110
                        +PKC GC +AI+  +  V    T WH  CF C +CK+          
Sbjct: 2   SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQ---------- 51

Query: 111 EGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCA 147
                       GSFF      YC T +  K  S  +
Sbjct: 52  --------VIGTGSFFPKGEDFYCVTCHETKFASGPS 80

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 69.7 bits (171), Expect = 3e-16
 Identities = 16/75 (21%), Positives = 27/75 (36%), Gaps = 2/75 (2%)

Query: 130 GLPYCETHYHAKRGSLCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQ 187
                      +    C GC K I    + +      +H + F C+ C + +  G+F  +
Sbjct: 2   SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPK 61

Query: 188 NDKPYCHGCFEKLFG 202
            +  YC  C E  F 
Sbjct: 62  GEDFYCVTCHETKFA 76

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 62.4 bits (152), Expect = 2e-13
 Identities = 13/50 (26%), Positives = 18/50 (36%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
          + V      WH + F C+ C +  G   F  K    YC   +   FA   
Sbjct: 30 QNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGP 79

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 78.5 bits (194), Expect = 8e-20
 Identities = 23/63 (36%), Positives = 32/63 (50%)

Query: 140 AKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEK 199
           +   S C  C KPIT   +T   + +H E FVC  C +QL+   F  ++D  YC  CF  
Sbjct: 2   SSGSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCD 61

Query: 200 LFG 202
           L+ 
Sbjct: 62  LYA 64

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 69.3 bits (170), Expect = 3e-16
 Identities = 18/52 (34%), Positives = 23/52 (44%)

Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
              VT  E+ WH E F C  C KQ     F  +D   YC + + DL+A   
Sbjct: 16 TTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGP 67

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 65.4 bits (160), Expect = 8e-15
 Identities = 17/85 (20%), Positives = 24/85 (28%), Gaps = 18/85 (21%)

Query: 63  DLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
              +  C  C + I    V+     WH  CFVC  C+K                     G
Sbjct: 2   SSGSSGCVQCKKPITTGGVTYREQPWHKECFVCTACRK------------------QLSG 43

Query: 123 GSFFDHEGLPYCETHYHAKRGSLCA 147
             F   +   YC   +     S  +
Sbjct: 44  QRFTARDDFAYCLNCFCDLYASGPS 68

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 77.5 bits (191), Expect = 3e-19
 Identities = 23/83 (27%), Positives = 29/83 (34%), Gaps = 18/83 (21%)

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
            P C  C   I+   V A +   H  CFVC DC                      +   +
Sbjct: 25  MPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNL------------------NLKQKGY 66

Query: 126 FDHEGLPYCETHYHAKRGSLCAG 148
           F  EG  YCETH  A+     +G
Sbjct: 67  FFVEGELYCETHARARTSGPSSG 89

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 71.0 bits (174), Expect = 1e-16
 Identities = 23/84 (27%), Positives = 30/84 (35%), Gaps = 3/84 (3%)

Query: 122 GGSFFDHEGLPYCETHYH---AKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQ 178
           G S       P  + H     A+R  LC  C   I G  + A  +  HPE FVCA C   
Sbjct: 1   GSSGSSGVRAPVTKVHGGAGSAQRMPLCDKCGSGIVGAVVKARDKYRHPECFVCADCNLN 60

Query: 179 LNKGTFKEQNDKPYCHGCFEKLFG 202
           L +  +     + YC         
Sbjct: 61  LKQKGYFFVEGELYCETHARARTS 84

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 67.9 bits (166), Expect = 2e-15
 Identities = 14/52 (26%), Positives = 20/52 (38%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGG 71
            V A +K  H E F CA C     + G+   +G+ YC        +    G
Sbjct: 38 AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSSG 89

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 76.0 bits (187), Expect = 1e-18
 Identities = 21/73 (28%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 132 PYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT--FKEQND 189
                 Y  K G  C GC   +TG  + A   K+HPE F C  C   +  G      Q+ 
Sbjct: 4   GSSGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHA 63

Query: 190 KPYCHGCFEKLFG 202
             YC  C  ++  
Sbjct: 64  TLYCGKCHNEVVS 76

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 71.0 bits (174), Expect = 9e-17
 Identities = 17/96 (17%), Positives = 28/96 (29%), Gaps = 16/96 (16%)

Query: 53  GKPYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEG 112
                  DY+  F   C GC+  +   ++ A   ++H  CF C  CK  +     Y    
Sbjct: 2   SSGSSGKDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAY---- 57

Query: 113 KPDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAG 148
                               YC   ++       +G
Sbjct: 58  ------------ALVQHATLYCGKCHNEVVSGPSSG 81

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 52.1 bits (125), Expect = 1e-09
 Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 9/72 (12%)

Query: 9  FDDHFSLRCFQ-------KCVTALEKTWHTEHFFCAQCGKQF--GEDGFHEKDGKPYCRD 59
          +   F   C           + A E  +H E F C  C      G+     +    YC  
Sbjct: 10 YWGKFGEFCHGCSLLMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGK 69

Query: 60 DYFDLFAPKCGG 71
           + ++ +    G
Sbjct: 70 CHNEVVSGPSSG 81

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B Length = 66

 Score = 75.0 bits (185), Expect = 1e-18
 Identities = 22/63 (34%), Positives = 33/63 (52%)

Query: 140 AKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEK 199
           +    +C  C +PI GR + AM +++H EHFVCA C +        E+    YC   + +
Sbjct: 2   SMGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQ 61

Query: 200 LFG 202
           LFG
Sbjct: 62  LFG 64

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B Length = 66

 Score = 73.9 bits (182), Expect = 4e-18
 Identities = 28/82 (34%), Positives = 37/82 (45%), Gaps = 18/82 (21%)

Query: 64  LFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGG 123
           +  P CG C R I    V+A+  QWH   FVC  C+K                  PF G 
Sbjct: 3   MGVPICGACRRPIEGRVVNAMGKQWHVEHFVCAKCEK------------------PFLGH 44

Query: 124 SFFDHEGLPYCETHYHAKRGSL 145
             ++ +GL YCETHY+   G +
Sbjct: 45  RHYERKGLAYCETHYNQLFGDV 66

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B Length = 66

 Score = 68.5 bits (168), Expect = 4e-16
 Identities = 20/48 (41%), Positives = 25/48 (52%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP 67
          + V A+ K WH EHF CA+C K F     +E+ G  YC   Y  LF  
Sbjct: 18 RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD 65

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 74.4 bits (183), Expect = 3e-18
 Identities = 18/84 (21%), Positives = 25/84 (29%), Gaps = 18/84 (21%)

Query: 65  FAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGS 124
             P C  C   I+  +V   +   H  C+VC DC                      +   
Sbjct: 14  KLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGT------------------NLKQKG 55

Query: 125 FFDHEGLPYCETHYHAKRGSLCAG 148
            F  E   YCE H   +     +G
Sbjct: 56  HFFVEDQIYCEKHARERVSGPSSG 79

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 66.7 bits (163), Expect = 3e-15
 Identities = 16/63 (25%), Positives = 24/63 (38%)

Query: 140 AKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEK 199
           A++  +C  C   I G  +    R  HPE +VC  C   L +       D+ YC     +
Sbjct: 12  AQKLPMCDKCGTGIVGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARE 71

Query: 200 LFG 202
              
Sbjct: 72  RVS 74

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 65.5 bits (160), Expect = 9e-15
 Identities = 10/52 (19%), Positives = 18/52 (34%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGG 71
            V   ++  H E + C  CG    + G    + + YC     +  +    G
Sbjct: 28 VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSSG 79

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 73.6 bits (181), Expect = 7e-18
 Identities = 17/93 (18%), Positives = 31/93 (33%), Gaps = 17/93 (18%)

Query: 55  PYCRDDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP 114
               +  +     KC  C++ I++  + A+   +H  CF C  C + + G  F       
Sbjct: 4   GSSGEGCYVATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFT------ 57

Query: 115 DCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCA 147
                       D     +C   +H K  S  +
Sbjct: 58  -----------VDATSQIHCIEDFHRKFASGPS 79

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 69.3 bits (170), Expect = 3e-16
 Identities = 18/72 (25%), Positives = 27/72 (37%), Gaps = 1/72 (1%)

Query: 132 PYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQL-NKGTFKEQNDK 190
                  +      CA C +PI  R + AM + +HP  F C  C R L       +   +
Sbjct: 4   GSSGEGCYVATLEKCATCSQPILDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQ 63

Query: 191 PYCHGCFEKLFG 202
            +C   F + F 
Sbjct: 64  IHCIEDFHRKFA 75

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 65.9 bits (161), Expect = 7e-15
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 1/51 (1%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFH-EKDGKPYCRDDYFDLFAPKC 69
          + + A+ K +H   F C  C +      F  +   + +C +D+   FA   
Sbjct: 28 RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGP 78

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 72.8 bits (179), Expect = 1e-17
 Identities = 19/61 (31%), Positives = 24/61 (39%)

Query: 142 RGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
             S C  C + I GR I AM   +HPE F C  C   L    F +   +  C  C  +  
Sbjct: 4   GSSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 63

Query: 202 G 202
            
Sbjct: 64  A 64

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 61.7 bits (150), Expect = 2e-13
 Identities = 15/82 (18%), Positives = 27/82 (32%), Gaps = 18/82 (21%)

Query: 66  APKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
           +  C  C   I+   + A+N  WH  CF C  C++                        F
Sbjct: 5   SSGCHQCGEFIIGRVIKAMNNSWHPECFRCDLCQE------------------VLADIGF 46

Query: 126 FDHEGLPYCETHYHAKRGSLCA 147
             + G   C   ++ ++ S  +
Sbjct: 47  VKNAGRHLCRPCHNREKASGPS 68

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 60.1 bits (146), Expect = 8e-13
 Identities = 13/50 (26%), Positives = 22/50 (44%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
          + + A+  +WH E F C  C +   + GF +  G+  CR  +    A   
Sbjct: 18 RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGP 67

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 71.7 bits (176), Expect = 4e-17
 Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 1/57 (1%)

Query: 145 LCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           +C  CH  I  + +      +HP+HF CA C ++L     +E   + YC  C +K+ 
Sbjct: 17  ICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELT-ADARELKGELYCLPCHDKMG 72

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 53.3 bits (128), Expect = 5e-10
 Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 1/50 (2%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
          + +      +H +HF CA CGK+   D   E  G+ YC   +  +     
Sbjct: 28 QPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMGVSGP 76

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 15/81 (18%), Positives = 24/81 (29%), Gaps = 19/81 (23%)

Query: 67  PKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSFF 126
             C  C+  I E  +   N  +H   F C +C K +T                       
Sbjct: 16  YICQKCHAIIDEQPLIFKNDPYHPDHFNCANCGKELT-------------------ADAR 56

Query: 127 DHEGLPYCETHYHAKRGSLCA 147
           + +G  YC   +     S  +
Sbjct: 57  ELKGELYCLPCHDKMGVSGPS 77

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 71.0 bits (174), Expect = 7e-17
 Identities = 18/71 (25%), Positives = 25/71 (35%), Gaps = 5/71 (7%)

Query: 53  GKPYCRDDYFDLFAPKCGGCNRAIM-----ENYVSALNTQWHSTCFVCRDCKKPVTGKSF 107
                 D Y +  A KC GC   I       + V+     WH  CF C+ C   +  K F
Sbjct: 2   SSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRF 61

Query: 108 YAMEGKPDCRQ 118
              + +  C  
Sbjct: 62  VFHQEQVYCPD 72

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 69.8 bits (171), Expect = 2e-16
 Identities = 20/76 (26%), Positives = 26/76 (34%), Gaps = 5/76 (6%)

Query: 130 GLPYCETHYHAKRGSLCAGCHKPITG-----RCITAMFRKFHPEHFVCAFCLRQLNKGTF 184
                   Y       CAGC  PITG       +    + +H   F C  C   L    F
Sbjct: 2   SSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRF 61

Query: 185 KEQNDKPYCHGCFEKL 200
               ++ YC  C +KL
Sbjct: 62  VFHQEQVYCPDCAKKL 77

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 51.3 bits (123), Expect = 2e-09
 Identities = 11/47 (23%), Positives = 15/47 (31%)

Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDL 64
              V    ++WH   F C +C        F     + YC D    L
Sbjct: 31 GSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL 77

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 69

 Score = 70.1 bits (172), Expect = 1e-16
 Identities = 18/57 (31%), Positives = 27/57 (47%)

Query: 146 CAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           C  C+K IT   IT   + +H + FVC  C ++L    F    D+ YC  C++    
Sbjct: 8   CVKCNKAITSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 69

 Score = 69.3 bits (170), Expect = 3e-16
 Identities = 13/54 (24%), Positives = 22/54 (40%)

Query: 18 FQKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGG 71
              +T  ++ WH + F C  C K+     F   + + YC D Y +  +    G
Sbjct: 16 TSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG 69

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 69

 Score = 68.2 bits (167), Expect = 6e-16
 Identities = 20/86 (23%), Positives = 27/86 (31%), Gaps = 18/86 (20%)

Query: 63  DLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
              +  C  CN+AI    ++  +  WH+ CFVC  C K                     G
Sbjct: 2   SSGSSGCVKCNKAITSGGITYQDQPWHADCFVCVTCSK------------------KLAG 43

Query: 123 GSFFDHEGLPYCETHYHAKRGSLCAG 148
             F   E   YC   Y        +G
Sbjct: 44  QRFTAVEDQYYCVDCYKNFVSGPSSG 69

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 69.7 bits (171), Expect = 2e-16
 Identities = 17/68 (25%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 137 HYHAKRGSLCAGCHKPIT--GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCH 194
           ++     + C  C        + + +    +H + FVCA C +Q  +G F E   + YC 
Sbjct: 5   YFQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCE 64

Query: 195 GCFEKLFG 202
             F+ LF 
Sbjct: 65  HDFQMLFA 72

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 62.4 bits (152), Expect = 1e-13
 Identities = 20/48 (41%), Positives = 30/48 (62%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA 66
          +K V +  + +H + F CAQC +QF E  F+E +G+ YC  D+  LFA
Sbjct: 25 EKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 60.1 bits (146), Expect = 1e-12
 Identities = 18/84 (21%), Positives = 27/84 (32%), Gaps = 20/84 (23%)

Query: 60  DYFDLFAPKCGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
            +    +  C  C       E  V++    +H  CFVC  C +                 
Sbjct: 5   YFQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQ----------------- 47

Query: 118 QPFQGGSFFDHEGLPYCETHYHAK 141
             F  G F++ EG  YCE  +   
Sbjct: 48  -QFPEGLFYEFEGRKYCEHDFQML 70

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 77

 Score = 69.7 bits (171), Expect = 2e-16
 Identities = 19/71 (26%), Positives = 30/71 (42%), Gaps = 2/71 (2%)

Query: 134 CETHYHAKRGSLCAGCHKPI--TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKP 191
            E   +A   + C  C        + + +    +H + FVCA C +Q  +G F E   + 
Sbjct: 2   SEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRK 61

Query: 192 YCHGCFEKLFG 202
           YC   F+ LF 
Sbjct: 62  YCEHDFQMLFA 72

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 77

 Score = 65.1 bits (159), Expect = 1e-14
 Identities = 21/51 (41%), Positives = 31/51 (60%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
          +K V +  + +H + F CAQC +QF E  F+E +G+ YC  D+  LFAP  
Sbjct: 25 EKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCW 75

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 77

 Score = 60.1 bits (146), Expect = 9e-13
 Identities = 19/87 (21%), Positives = 27/87 (31%), Gaps = 20/87 (22%)

Query: 57  CRDDYFDLFAPKCGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP 114
                  L +  C  C       E  V++    +H  CFVC  C +              
Sbjct: 2   SEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQ-------------- 47

Query: 115 DCRQPFQGGSFFDHEGLPYCETHYHAK 141
                F  G F++ EG  YCE  +   
Sbjct: 48  ----QFPEGLFYEFEGRKYCEHDFQML 70

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 68.7 bits (168), Expect = 7e-16
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 1/67 (1%)

Query: 137 HYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT-FKEQNDKPYCHG 195
            Y    G+ C  C + I G  ++A+ + +HP+ FVCA C      G        +  C  
Sbjct: 9   DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68

Query: 196 CFEKLFG 202
           C   +  
Sbjct: 69  CSLPVSV 75

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 68.3 bits (167), Expect = 9e-16
 Identities = 21/69 (30%), Positives = 27/69 (39%), Gaps = 4/69 (5%)

Query: 60  DYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKP----D 115
           DY  L+  +C  C++ I    VSAL   +H  CFVC  C+ P          GK      
Sbjct: 9   DYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68

Query: 116 CRQPFQGGS 124
           C  P     
Sbjct: 69  CSLPVSVSG 77

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 47.9 bits (114), Expect = 4e-08
 Identities = 15/66 (22%), Positives = 24/66 (36%), Gaps = 8/66 (12%)

Query: 9  FDDHFSLRCFQ-------KCVTALEKTWHTEHFFCAQCGKQFGEDGFH-EKDGKPYCRDD 60
          +   +  RCF        + V+AL KT+H + F CA C   F           +  C+  
Sbjct: 10 YQRLYGTRCFSCDQFIEGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKC 69

Query: 61 YFDLFA 66
             +  
Sbjct: 70 SLPVSV 75

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 67.5 bits (165), Expect = 2e-15
 Identities = 25/89 (28%), Positives = 36/89 (40%), Gaps = 20/89 (22%)

Query: 60  DYFDLFAPKCGGCNRAIME-NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
                    C GC   I     + AL+ QWH +CF C+ C   +TG              
Sbjct: 9   PIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-------------- 54

Query: 119 PFQGGSFFDHEGLPYCETHYHAKRGSLCA 147
                 +   +G+PYCE+ YHA+ GS  +
Sbjct: 55  -----EYISKDGVPYCESDYHAQFGSGPS 78

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 59.8 bits (145), Expect = 2e-12
 Identities = 17/49 (34%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
           + AL+K WH   F C  C        +  KDG PYC  DY   F    
Sbjct: 30 SLLALDKQWHVSCFKCQTCSVIL-TGEYISKDGVPYCESDYHAQFGSGP 77

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 57.1 bits (138), Expect = 1e-11
 Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 138 YHAKRGSLCAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGC 196
              +  S CAGC + I  G+ + A+ +++H   F C  C   L  G +  ++  PYC   
Sbjct: 10  IKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESD 68

Query: 197 FEKLFG 202
           +   FG
Sbjct: 69  YHAQFG 74

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 65.1 bits (159), Expect = 1e-14
 Identities = 23/61 (37%), Positives = 28/61 (45%), Gaps = 1/61 (1%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDD-YFDLFAPKCGGCNRAIMEN 79
           VT+L K WH     C +CGK     G  E +GKPYC    Y  +F PK  G   A    
Sbjct: 15 RVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAESHT 74

Query: 80 Y 80
          +
Sbjct: 75 F 75

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 56.2 bits (136), Expect = 3e-11
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 146 CAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC-HGCFEKLFG 202
           C  C K +     +T++ + +H     C  C + L  G   E   KPYC H C+  +FG
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 67  PKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119
           PKC  C++ +     V++L   WH  C  C  C K +T       EGKP C  P
Sbjct: 1   PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHP 54

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 63.9 bits (156), Expect = 3e-14
 Identities = 14/51 (27%), Positives = 20/51 (39%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
           + +    +TWH   F C+ C +  G   F    G  YC   Y + FA   
Sbjct: 19 SRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGP 69

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 63.5 bits (155), Expect = 5e-14
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 144 SLCAGCHKPIT--GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           S C+ C + +    R +    + +H   F+C+ C + L   +F       YC  C+E  F
Sbjct: 6   SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 65

Query: 202 G 202
            
Sbjct: 66  A 66

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 60.5 bits (147), Expect = 6e-13
 Identities = 18/85 (21%), Positives = 26/85 (30%), Gaps = 20/85 (23%)

Query: 65  FAPKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
            +  C  C   +M     +      WH  CF+C  C++                  P   
Sbjct: 4   GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQ------------------PLGS 45

Query: 123 GSFFDHEGLPYCETHYHAKRGSLCA 147
            SF   +G  YC   Y  K  S  +
Sbjct: 46  RSFVPDKGAHYCVPCYENKFASGPS 70

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 65.0 bits (158), Expect = 5e-14
 Identities = 25/114 (21%), Positives = 40/114 (35%), Gaps = 16/114 (14%)

Query: 21  CVTALEKTWHTEHFFCAQCGKQFGEDG--FHEKDGKPYCRDDYFDLFAPKCGGCNRAIME 78
            + A++  WH+    C+ C  Q G+ G   + K G   CR+DY  LF     G +   M 
Sbjct: 20  LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMG 79

Query: 79  NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR---QPFQGGSFFDHE 129
           +              V  +    + G  F   + +   R     F   +  D E
Sbjct: 80  SGG---------DVMVVGEP--TLMGGEFGDEDERLITRLENTQFDAANGIDDE 122

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 63.8 bits (155), Expect = 1e-13
 Identities = 24/141 (17%), Positives = 42/141 (29%), Gaps = 30/141 (21%)

Query: 64  LFAPKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
           L   +C GC   I + ++  A+++ WHS C  C  C+  +                   G
Sbjct: 3   LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGD----------------IG 46

Query: 123 GSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKG 182
            S +   G+  C   Y    G+  AG      G     M                    G
Sbjct: 47  TSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDVM------------VVGEPTLMG 94

Query: 183 -TFKEQNDKPYCHGCFEKLFG 202
             F +++++        +   
Sbjct: 95  GEFGDEDERLITRLENTQFDA 115

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 63.2 bits (154), Expect = 5e-14
 Identities = 12/50 (24%), Positives = 19/50 (38%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKC 69
          + +     +WH   F C +C +  G   F  KD + +C   Y    A   
Sbjct: 20 RKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGP 69

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 61.3 bits (149), Expect = 3e-13
 Identities = 15/65 (23%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 140 AKRGSLCAGCHKPIT--GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCF 197
           +   S C  C K I    R +      +H   F+C  C + +   +F  ++++ +C  C+
Sbjct: 2   SSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCY 61

Query: 198 EKLFG 202
           EK   
Sbjct: 62  EKQHA 66

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 58.9 bits (143), Expect = 2e-12
 Identities = 17/85 (20%), Positives = 28/85 (32%), Gaps = 20/85 (23%)

Query: 65  FAPKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQG 122
            +  C  C + IM     +    + WH TCF+C  C++                  P   
Sbjct: 4   GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQ------------------PIGT 45

Query: 123 GSFFDHEGLPYCETHYHAKRGSLCA 147
            SF   +   +C   Y  +  S  +
Sbjct: 46  KSFIPKDNQNFCVPCYEKQHASGPS 70

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 63.3 bits (154), Expect = 7e-14
 Identities = 13/68 (19%), Positives = 24/68 (35%), Gaps = 2/68 (2%)

Query: 53  GKPYCRDDYFDLFAPKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAM 110
                   Y + FA  C  C + I      +   +  +H  CF C  C++ +  + F   
Sbjct: 2   SSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQ 61

Query: 111 EGKPDCRQ 118
           + +  C  
Sbjct: 62  DSELLCND 69

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 62.9 bits (153), Expect = 9e-14
 Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 2/73 (2%)

Query: 132 PYCETHYHAKRGSLCAGCHKPITG--RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQND 189
                 Y     + CA C + I    R +    R FH   F C  C R L    F  Q+ 
Sbjct: 4   GSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDS 63

Query: 190 KPYCHGCFEKLFG 202
           +  C+ C+   F 
Sbjct: 64  ELLCNDCYCSAFS 76

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 59.0 bits (143), Expect = 3e-12
 Identities = 13/70 (18%), Positives = 28/70 (40%), Gaps = 9/70 (12%)

Query: 9  FDDHFSLRCF---------QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRD 59
          +D+ F+  C           + +   ++ +H   F C +C +   ++ F  +D +  C D
Sbjct: 10 YDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCND 69

Query: 60 DYFDLFAPKC 69
           Y   F+   
Sbjct: 70 CYCSAFSSGP 79

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 62.5 bits (152), Expect = 1e-13
 Identities = 12/51 (23%), Positives = 19/51 (37%), Gaps = 1/51 (1%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGC 72
          V AL++ +H   F C+ C  Q     F+  + + YC   Y           
Sbjct: 22 VVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE-SGPSS 71

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 59.4 bits (144), Expect = 2e-12
 Identities = 24/86 (27%), Positives = 34/86 (39%), Gaps = 21/86 (24%)

Query: 66  APKCGGCNRAIM--ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGG 123
           +  CGGC   ++     V AL+  +H  CFVC  C+  + G+ FYA+E +          
Sbjct: 5   SSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERR---------- 54

Query: 124 SFFDHEGLPYCETHYHAKRGSLCAGC 149
                    YCE  Y A   S     
Sbjct: 55  --------AYCEGCYVATLES-GPSS 71

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 59.0 bits (143), Expect = 2e-12
 Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 146 CAGCHKPITGRC--ITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           C GC + + G    + A+ R FH   FVC+ C  QL    F     + YC GC+    
Sbjct: 8   CGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL 65

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A Length = 81

 Score = 61.7 bits (150), Expect = 3e-13
 Identities = 13/51 (25%), Positives = 19/51 (37%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGC 72
          V    +++H   F C  C K          D + YC+  Y   + PK  G 
Sbjct: 23 VQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGY 73

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A Length = 81

 Score = 57.0 bits (138), Expect = 2e-11
 Identities = 19/85 (22%), Positives = 28/85 (32%), Gaps = 19/85 (22%)

Query: 66  APKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGS 124
             KCG C R +     V      +H  CF+C  C+K +                     +
Sbjct: 7   GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDS------------------TT 48

Query: 125 FFDHEGLPYCETHYHAKRGSLCAGC 149
              H+   YC++ Y  K G    G 
Sbjct: 49  VAIHDAEVYCKSCYGKKYGPKGYGY 73

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A Length = 81

 Score = 56.6 bits (137), Expect = 2e-11
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 143 GSLCAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           G+ C  C + +     +    R FH   F+C  C + L+  T    + + YC  C+ K +
Sbjct: 7   GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKY 66

Query: 202 G 202
           G
Sbjct: 67  G 67

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 61.0 bits (148), Expect = 4e-13
 Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 4/58 (6%)

Query: 64  LFAPKCGGCNRAIM----ENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCR 117
             +  C GC   I       Y+S    QWH+ CF C+ C   + G+ F        C 
Sbjct: 3   SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCP 60

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 60.2 bits (146), Expect = 9e-13
 Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 4/61 (6%)

Query: 146 CAGCHKPITG----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           CAGC  PI+G    + I+   R++H + F C  C   L    F  + D   C  C + + 
Sbjct: 8   CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDIS 67

Query: 202 G 202
           G
Sbjct: 68  G 68

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 59.5 bits (144), Expect = 2e-12
 Identities = 14/52 (26%), Positives = 21/52 (40%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCG 70
           K ++  E+ WH + F C +C       GF  +     C D   D+  P  G
Sbjct: 21 TKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSSG 72

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 60.6 bits (147), Expect = 6e-13
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 4/60 (6%)

Query: 63  DLFAPKCGGCNRAIME----NYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQ 118
              +  C  C++ I       ++   ++QWHS CF C  C   + GK F     +  C++
Sbjct: 2   SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQK 61

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 57.9 bits (140), Expect = 7e-12
 Identities = 18/60 (30%), Positives = 25/60 (41%), Gaps = 4/60 (6%)

Query: 146 CAGCHKPITG----RCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           C  C KPI+G    + I     ++H E F C  C   L    F  QN + +C  C   + 
Sbjct: 8   CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMD 67

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 52.6 bits (126), Expect = 8e-10
 Identities = 11/55 (20%), Positives = 22/55 (40%)

Query: 19 QKCVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCN 73
           K +   +  WH+E F C +C       GF  ++ + +C+     +     G  +
Sbjct: 21 AKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS 75

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 62.0 bits (150), Expect = 6e-13
 Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 6/93 (6%)

Query: 22  VTALEKTWHTEHFFCAQCGKQFGEDG--FHEKDGKPYCRDDYFDLFAPKCGGCNRAIM-- 77
           + A+++ WH +   C  CG + GE G   + K G+  CR DY  L        +   +  
Sbjct: 19  LKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDVMV 78

Query: 78  --ENYVSALNTQWHSTCFVCRDCKKPVTGKSFY 108
             E  +            + R         +  
Sbjct: 79  VGEPTLMGGEFGDEDERLITRLENTQFDAANGI 111

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 59.3 bits (143), Expect = 6e-12
 Identities = 20/127 (15%), Positives = 30/127 (23%), Gaps = 21/127 (16%)

Query: 67  PKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGSF 125
             CGGC + I + Y   A++  WH  C  C  C   +                   G   
Sbjct: 4   LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRL----------------GEVGRRL 47

Query: 126 FDHEGLPYCETHYHAKRGSLCAGCHKPITGRC----ITAMFRKFHPEHFVCAFCLRQLNK 181
           +   G   C   Y    GS                 +         E  +      Q + 
Sbjct: 48  YYKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDA 107

Query: 182 GTFKEQN 188
               +  
Sbjct: 108 ANGIDDE 114

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens} Length = 123

 Score = 59.4 bits (143), Expect = 6e-12
 Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)

Query: 21  CVTALEKTWHTEHFFCAQCGKQFGEDGF--HEKDGKPYCRDDYFDLFA 66
            + A++  WH+    C+ C  Q G+ G   + K G   CR+DY  LF 
Sbjct: 76  LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 123

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens} Length = 123

 Score = 58.2 bits (140), Expect = 1e-11
 Identities = 19/92 (20%), Positives = 26/92 (28%), Gaps = 3/92 (3%)

Query: 114 PDCRQPFQGGSFFDHEGLPYCETHYHAKRGSLCAGCHKPITGR-CITAMFRKFHPEHFVC 172
                   G       G               CAGC   I  R  + AM   +H     C
Sbjct: 32  VTVIDTKDGSQSKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKC 91

Query: 173 AFCLRQLNKGTFK--EQNDKPYCHGCFEKLFG 202
           + C  QL         ++    C   + +LFG
Sbjct: 92  SSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 123

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens} Length = 123

 Score = 57.1 bits (137), Expect = 4e-11
 Identities = 18/93 (19%), Positives = 29/93 (31%), Gaps = 17/93 (18%)

Query: 52  DGKPYCRDDYFDLFAPKCGGCNRAIMENYV-SALNTQWHSTCFVCRDCKKPVTGKSFYAM 110
            G          L   +C GC   I + ++  A+++ WHS C  C  C+  +        
Sbjct: 47  GGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGT--- 103

Query: 111 EGKPDCRQPFQGGSFFDHEGLPYCETHYHAKRG 143
                        S +   G+  C   Y    G
Sbjct: 104 -------------SSYTKSGMILCRNDYIRLFG 123

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 56.3 bits (136), Expect = 3e-11
 Identities = 16/59 (27%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 146 CAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYC-HGCFEKLFG 202
           C  C K +     ++++ + +H     C  C + L  G   E + KP+C   C+  LFG
Sbjct: 12  CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG 70

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 17/50 (34%), Positives = 22/50 (44%), Gaps = 1/50 (2%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFD-LFAPKC 69
           V++L K WH     C +C K     G  E DGKP+C    +  LF    
Sbjct: 24 KVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGP 73

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 48.5 bits (116), Expect = 2e-08
 Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 1/55 (1%)

Query: 66  APKCGGCNRAIMEN-YVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQP 119
           A KC  C++ +     VS+L   WH  C  C  C K +T       +GKP C +P
Sbjct: 9   ASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKP 63

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 91

 Score = 51.8 bits (124), Expect = 2e-09
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 146 CAGCHKPIT-GRCITAMFRKFHPEHFVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           C  C K +     + A  + FH   F C++C  +L+ GT+   + + YC   F +LF 
Sbjct: 18  CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFK 75

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 91

 Score = 51.0 bits (122), Expect = 4e-09
 Identities = 11/51 (21%), Positives = 21/51 (41%)

Query: 22 VTALEKTWHTEHFFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGC 72
          + A ++ +H   F C+ C  +     +    G+ YC+  +  LF  K    
Sbjct: 31 LLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 81

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 91

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 17/92 (18%), Positives = 30/92 (32%), Gaps = 21/92 (22%)

Query: 66  APKCGGCNRAI--MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGG 123
              C  C + +  ME  + A    +H +CF C  C   ++                   G
Sbjct: 15  RETCVECQKTVYPME-RLLANQQVFHISCFRCSYCNNKLS------------------LG 55

Query: 124 SFFDHEGLPYCETHYHAKRGSLCAGCHKPITG 155
           ++    G  YC+ H++    S         +G
Sbjct: 56  TYASLHGRIYCKPHFNQLFKSKGNYDEGFGSG 87

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 47.0 bits (111), Expect = 7e-08
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 143 GSLCAGCHKPITGRCITAMFRKFHPEHFVCAFCLRQLNKGT-FKEQNDKPYCHGCFEK 199
            S C  C K ITGR + A  + +HP   +C  C +   +G     Q    +   C + 
Sbjct: 5   SSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQA 62

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 40.1 bits (93), Expect = 2e-05
 Identities = 13/62 (20%), Positives = 23/62 (37%), Gaps = 4/62 (6%)

Query: 65  FAPKCGGCNRAIMENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGK----PDCRQPF 120
            +  C  C + I    + A    +H +C +C  C +         ++G     P CRQ  
Sbjct: 4   GSSGCDSCEKYITGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAA 63

Query: 121 QG 122
           + 
Sbjct: 64  RT 65

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 36.2 bits (83), Expect = 6e-04
 Identities = 9/41 (21%), Positives = 18/41 (43%), Gaps = 1/41 (2%)

Query: 20 KCVTALEKTWHTEHFFCAQCGKQFGE-DGFHEKDGKPYCRD 59
          + + A EK +H     C +CG+ F E +  + +    +   
Sbjct: 18 RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPA 58

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens} Length = 65

 Score = 41.0 bits (96), Expect = 9e-06
 Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 4/56 (7%)

Query: 65  FAPKCGGCNRAIM--ENYVSALNTQWHST--CFVCRDCKKPVTGKSFYAMEGKPDC 116
            A  C GC+ AI      V+  N  WH++  CF+C  C K + G+ F  +EG   C
Sbjct: 1   HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFC 56

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 40.3 bits (94), Expect = 3e-05
 Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 3/68 (4%)

Query: 137 HYHAKRGSLCAGCHKPI-TGRCITAMFRKFHPEHFVCAFCLRQLNKGTFK--EQNDKPYC 193
           H  A  G LCA C + +     +      FH   F C  C   L  G ++    +   YC
Sbjct: 9   HQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYC 68

Query: 194 HGCFEKLF 201
                +  
Sbjct: 69  LQHLPQTD 76

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 11/53 (20%), Positives = 15/53 (28%), Gaps = 2/53 (3%)

Query: 21 CVTALEKTWHTEHFFCAQCGKQFGEDGF--HEKDGKPYCRDDYFDLFAPKCGG 71
           +      +H   F C  C       G+  H  DG  YC        +    G
Sbjct: 30 RLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPSSG 82

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 38.8 bits (90), Expect = 9e-05
 Identities = 11/74 (14%), Positives = 20/74 (27%), Gaps = 17/74 (22%)

Query: 66  APKCGGCNRAI-MENYVSALNTQWHSTCFVCRDCKKPVTGKSFYAMEGKPDCRQPFQGGS 124
              C  C   + +   +      +H +CF C  C+  +    +                 
Sbjct: 15  GDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGY----------------E 58

Query: 125 FFDHEGLPYCETHY 138
               +G  YC  H 
Sbjct: 59  QHPGDGHFYCLQHL 72

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	202
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	1e-11
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	2e-05
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	4e-09
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	4e-08
d1x3ha2	32	g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens)	7e-09
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	1e-08
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	1e-04
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	0.002
d1u5sb1	31	g.39.1.3 (B:72-102) Pinch (particularly interestin	1e-08
d1u5sb1	31	g.39.1.3 (B:72-102) Pinch (particularly interestin	4e-04
d1b8ta2	65	g.39.1.3 (A:36-100) Cysteine-rich (intestinal) pro	9e-05
d1b8ta4	49	g.39.1.3 (A:144-192) Cysteine-rich (intestinal) pr	3e-04
d1b8ta4	49	g.39.1.3 (A:144-192) Cysteine-rich (intestinal) pr	4e-04
d1v6ga1	41	g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abL	0.001
d1x63a1	37	g.39.1.3 (A:8-44) Four and a half LIM domains prot	0.002

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.1 bits (133), Expect = 1e-11
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 140 AKRGSLCAGCHKPITGRCITAMFRKFHPEHF 170
            KR  +CA C++ I G  + A+ + +HPE F
Sbjct: 15  GKRTPMCAHCNQVIRGPFLVALGKSWHPEEF 45

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.6 bits (90), Expect = 2e-05
 Identities = 10/27 (37%), Positives = 13/27 (48%)

Query: 67 PKCGGCNRAIMENYVSALNTQWHSTCF 93
          P C  CN+ I   ++ AL   WH   F
Sbjct: 19 PMCAHCNQVIRGPFLVALGKSWHPEEF 45

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.5 bits (116), Expect = 4e-09
 Identities = 20/34 (58%), Positives = 28/34 (82%)

Query: 60 DYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCF 93
          D+  +F+PKCGGCNR ++ENY+SA++T WH  CF
Sbjct: 2  DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF 35

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.4 bits (108), Expect = 4e-08
 Identities = 11/34 (32%), Positives = 18/34 (52%)

Query: 137 HYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHF 170
            + A     C GC++P+    ++AM   +HPE F
Sbjct: 2   DFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF 35

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 32

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.4 bits (113), Expect = 7e-09
 Identities = 16/29 (55%), Positives = 20/29 (68%)

Query: 115 DCRQPFQGGSFFDHEGLPYCETHYHAKRG 143
           DC   F  GSFF+ +G P+CE HYH +RG
Sbjct: 4   DCFTSFSTGSFFELDGRPFCELHYHHRRG 32

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.0 bits (112), Expect = 1e-08
 Identities = 18/34 (52%), Positives = 23/34 (67%)

Query: 34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP 67
          F CAQC +QF E  F+E +G+ YC  D+  LFAP
Sbjct: 1  FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP 34

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 35.8 bits (83), Expect = 1e-04
 Identities = 10/25 (40%), Positives = 13/25 (52%)

Query: 115 DCRQPFQGGSFFDHEGLPYCETHYH 139
            C Q F  G F++ EG  YCE  + 
Sbjct: 5   QCFQQFPEGLFYEFEGRKYCEHDFQ 29

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (75), Expect = 0.002
 Identities = 14/32 (43%), Positives = 18/32 (56%)

Query: 170 FVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLF 201
           FVCA C +Q  +G F E   + YC   F+ LF
Sbjct: 1   FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 32

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 31

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.7 bits (111), Expect = 1e-08
 Identities = 11/26 (42%), Positives = 17/26 (65%)

Query: 144 SLCAGCHKPITGRCITAMFRKFHPEH 169
            +C  C +PI GR + AM +++H EH
Sbjct: 6   PICGACRRPIEGRVVNAMGKQWHVEH 31

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]} Length = 31

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.3 bits (79), Expect = 4e-04
 Identities = 11/26 (42%), Positives = 14/26 (53%)

Query: 64 LFAPKCGGCNRAIMENYVSALNTQWH 89
          +  P CG C R I    V+A+  QWH
Sbjct: 3  MGVPICGACRRPIEGRVVNAMGKQWH 28

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 65

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 37.1 bits (86), Expect = 9e-05
 Identities = 10/32 (31%), Positives = 16/32 (50%)

Query: 171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           +C  C + L+  T     D+ YC  C+ K +G
Sbjct: 1   LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYG 32

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 49

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 35.5 bits (82), Expect = 3e-04
 Identities = 15/37 (40%), Positives = 19/37 (51%)

Query: 36 CAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGC 72
          CA+CGK        +KDG+ YC+  Y   F PK  G 
Sbjct: 2  CAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGF 38

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 49

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

 Score = 34.7 bits (80), Expect = 4e-04
 Identities = 12/31 (38%), Positives = 18/31 (58%)

Query: 172 CAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG 202
           CA C + L   T  +++ + YC GC+ K FG
Sbjct: 2   CAKCGKSLESTTLADKDGEIYCKGCYAKNFG 32

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]} Length = 41

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 33.6 bits (77), Expect = 0.001
 Identities = 9/31 (29%), Positives = 17/31 (54%)

Query: 138 YHAKRGSLCAGCHKPITGRCITAMFRKFHPE 168
           Y    G+ C  C + I G  ++A+ + +HP+
Sbjct: 10  YQRLYGTRCFSCDQFIEGEVVSALGKTYHPD 40

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]} Length = 37

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.8 bits (75), Expect = 0.002
 Identities = 13/35 (37%), Positives = 17/35 (48%), Gaps = 2/35 (5%)

Query: 61 YFDLFAPKCGGCNRAIM--ENYVSALNTQWHSTCF 93
               +PKC GC +AI+  +  V    T WH  CF
Sbjct: 3  TTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF 37

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	202
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.36
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.29
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	99.05
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.9
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.88
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.85
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.82
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.81
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.8
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.77
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.71
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.71
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.7
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.67
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.66
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.64
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.63
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.63
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.62
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.6
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.6
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.58
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.58
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.55
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.53
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.49
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.49
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.45
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.44
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.42
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.41
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	98.36
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.36
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.36
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.35
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.33
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.31
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.31
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.28
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.27
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.26
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.26
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.25
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.24
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.21
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.19
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.18
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.18
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.07
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.04
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.04
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.97
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.95
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.94
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.94
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.91
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.91
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.9
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.9
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.89
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.85
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.83
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.82
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.78
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.78
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.74
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.72
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.69
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.64
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.63
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.61
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.61
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.6
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.58
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.53
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.53
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.52
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.5
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.49
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.48
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.46
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.45
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.44
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.42
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.39
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.37
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.37
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.34
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.21
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.16
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.15
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.11
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.09
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.06
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	96.99
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.99
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.97
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.96
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.95
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.94
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.77
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.7
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.48
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.43
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.32
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.22
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	96.13
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.11
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	95.48
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.42
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.32
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	95.32
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	95.06
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	94.8
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.72
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	94.62
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	94.41
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	94.01
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	93.84
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	93.69
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	93.54
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	93.32
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	93.11
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	92.67
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	92.39
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	91.2
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	91.08
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	91.04
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	90.05
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	89.45
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	84.83
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	80.46

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.36  E-value=1.5e-13  Score=73.60  Aligned_cols=35  Identities=31%  Similarity=0.702  Sum_probs=33.3

Q ss_pred             ccccccCCCCCCCCCCCcccceeeecCcccccccc
Q psy3653         136 THYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       136 ~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      ++|.++++++|.+|++||.|++|+|+|+.||++||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccchheeecCCccCcccC
Confidence            46889999999999999999999999999999998

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.29  E-value=4.3e-13  Score=71.84  Aligned_cols=35  Identities=57%  Similarity=1.438  Sum_probs=33.8

Q ss_pred             ccccccCCCCCcccccccccccccccCceecccCC
Q psy3653          59 DDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        59 ~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      +||.++|+|+|++|+++|.+++|+|+|+.||++||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSSCEEETTEEECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccchheeecCCccCcccC
Confidence            48999999999999999999999999999999998

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.05  E-value=1.4e-11  Score=65.71  Aligned_cols=34  Identities=53%  Similarity=0.986  Sum_probs=32.7

Q ss_pred             ccccccccccCCCceeeeCCeeeccccccccCCC
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP   67 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~   67 (202)
                      |+|+.|+++|.+..|+++||+|||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7899999999999999999999999999999987

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.90  E-value=4.2e-10  Score=58.31  Aligned_cols=35  Identities=29%  Similarity=0.432  Sum_probs=32.6

Q ss_pred             ccccccCCCCCCCCCCCcccceeeecCcccccccc
Q psy3653         136 THYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       136 ~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      +||.++++++|..|+++|+...|+..++.||++||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             CchHHHHHHHHhhcCCccccCceeecCCcchhhhC
Confidence            37888999999999999988889999999999998

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=3.3e-10  Score=60.22  Aligned_cols=33  Identities=42%  Similarity=0.907  Sum_probs=31.7

Q ss_pred             ccccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         170 FVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       170 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      |+|+.|+++|.++.|+++||+|||..||.++|+
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFA   33 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   33 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcC
Confidence            789999999999999999999999999999996

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=7.2e-10  Score=57.70  Aligned_cols=34  Identities=38%  Similarity=0.676  Sum_probs=29.8

Q ss_pred             ccccccCCCCCCCCCCCcccceeeecCcccccccc
Q psy3653         136 THYHAKRGSLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       136 ~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      .||.. ..++|..|+++|.++++.|.|+.|||.||
T Consensus         2 ~Cy~~-tlEkC~~C~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           2 GCYVA-TLEKCATCSQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCS-SCCBCTTTCCBCCSCCEEETTEEECTTTC
T ss_pred             hhHHH-HHHHHHHhchHHHHHHHHHhCCCCCCCCC
Confidence            34543 57899999999999999999999999998

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.82  E-value=8.5e-10  Score=62.51  Aligned_cols=40  Identities=38%  Similarity=0.764  Sum_probs=37.3

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCCCCCccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNR   74 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~   74 (202)
                      +|..|++.|++.+..++||+|||+.||.++|+|+..+.+.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~   40 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQ   40 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCccc
Confidence            6899999999999999999999999999999999988764

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.81  E-value=1.1e-09  Score=55.91  Aligned_cols=32  Identities=38%  Similarity=0.899  Sum_probs=30.3

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      .|..|+++|.+++|+.+|++|||..||+.+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            48899999999999999999999999999996

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=9e-10  Score=60.77  Aligned_cols=28  Identities=36%  Similarity=0.827  Sum_probs=26.9

Q ss_pred             CCCCCCCCCCcccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      .+.|+.|++||.|++|+|+|+.||++||
T Consensus        18 ~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CeeccccCCcccCceeeecCCccCcCCC
Confidence            5789999999999999999999999998

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.77  E-value=1.7e-09  Score=55.97  Aligned_cols=35  Identities=29%  Similarity=0.787  Sum_probs=32.9

Q ss_pred             ccccccCCCCCcccccccccccccccCceecccCC
Q psy3653          59 DDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        59 ~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      +||++.|+++|..|+++|+..-|...+..||.+||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSCCEESSSSEECTTTC
T ss_pred             CchHHHHHHHHhhcCCccccCceeecCCcchhhhC
Confidence            58999999999999999998888999999999998

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=3.7e-09  Score=56.39  Aligned_cols=35  Identities=20%  Similarity=0.398  Sum_probs=31.3

Q ss_pred             ccccccCCCCCCCCCCCcc--cceeeecCcccccccc
Q psy3653         136 THYHAKRGSLCAGCHKPIT--GRCITAMFRKFHPEHF  170 (202)
Q Consensus       136 ~~~~~~~~~~C~~C~~~I~--~~~~~~~~~~~H~~Cf  170 (202)
                      +||.+.++++|.+|++||.  ++.|.+.|+.||.+||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CccccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            3677889999999999994  5789999999999998

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=3.4e-09  Score=53.59  Aligned_cols=32  Identities=41%  Similarity=1.049  Sum_probs=30.1

Q ss_pred             cccccccccCCCceEeeCCcccCh-hhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCH-GCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~-~c~~~~fg  202 (202)
                      +|..|++.|..+...++||+|||. +||..+||
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            689999999999999999999995 69999998

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=3.6e-09  Score=53.15  Aligned_cols=32  Identities=38%  Similarity=0.951  Sum_probs=30.4

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      .|..|+++|.+++|..+|..|||.+||..+|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            48999999999999999999999999999996

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.67  E-value=4.8e-09  Score=59.35  Aligned_cols=32  Identities=38%  Similarity=0.922  Sum_probs=30.6

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      +|..|++.|++....++|++|||+.||.++||
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fG   32 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFG   32 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccC
Confidence            69999999999999999999999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.66  E-value=6.4e-09  Score=56.24  Aligned_cols=35  Identities=26%  Similarity=0.632  Sum_probs=32.9

Q ss_pred             cccccccCCCCCCCCCCCcccceeeecCccccccc
Q psy3653         135 ETHYHAKRGSLCAGCHKPITGRCITAMFRKFHPEH  169 (202)
Q Consensus       135 ~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~C  169 (202)
                      ..+|.++++.+|..|++-|++++|+|.+++|||.|
T Consensus         7 ~~DYq~~fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           7 GLDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             CSCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             cccHHHHhCcccccccCEeeeeeeEecCcccCCCC
Confidence            45799999999999999999999999999999987

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.64  E-value=5.4e-09  Score=52.42  Aligned_cols=31  Identities=35%  Similarity=0.831  Sum_probs=27.8

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      +|.+|++.|.. .|..+||.|||+.||...|+
T Consensus         1 kC~~C~~vL~g-EYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILTG-EYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCSS-CCEEETTEEECTTHHHHHTT
T ss_pred             CccccCccccc-eeecCCCCcccHHHHHHhcC
Confidence            68999999976 59999999999999998875

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=6.4e-09  Score=55.45  Aligned_cols=35  Identities=37%  Similarity=0.715  Sum_probs=32.3

Q ss_pred             ccccccCCCCCcccccccc--cccccccCceecccCC
Q psy3653          59 DDYFDLFAPKCGGCNRAIM--ENYVSALNTQWHSTCF   93 (202)
Q Consensus        59 ~c~~~~~~~~C~~C~~~I~--~~~v~~~~~~~H~~Cf   93 (202)
                      +||.+.++++|.+|+++|.  ++.|++.+..||..||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CccccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            4899999999999999997  5689999999999998

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=3.6e-09  Score=53.27  Aligned_cols=29  Identities=38%  Similarity=0.854  Sum_probs=26.3

Q ss_pred             cCCCCCCCCCCCcccceeeecCccccccc
Q psy3653         141 KRGSLCAGCHKPITGRCITAMFRKFHPEH  169 (202)
Q Consensus       141 ~~~~~C~~C~~~I~~~~~~~~~~~~H~~C  169 (202)
                      ++.++|+.|++||.++.|+|+|+.||+++
T Consensus         3 mg~p~C~~C~~PI~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEECCSCEECCTTSBEETTT
T ss_pred             cCCcchhhcCCchhhhHhhhhccccCCCC
Confidence            45688999999999999999999999974

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.62  E-value=7e-09  Score=57.93  Aligned_cols=32  Identities=41%  Similarity=1.030  Sum_probs=30.5

Q ss_pred             cccccccccCCCceEeeCCcccC-hhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYC-HGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC-~~c~~~~fg  202 (202)
                      +|..|++.|+++...++|++||| ++||.++||
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FG   33 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG   33 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccC
Confidence            68999999999999999999999 789999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.60  E-value=8.8e-09  Score=55.68  Aligned_cols=34  Identities=35%  Similarity=0.717  Sum_probs=32.6

Q ss_pred             ccccccCCCCCcccccccccccccccCceecccC
Q psy3653          59 DDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTC   92 (202)
Q Consensus        59 ~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~C   92 (202)
                      .||.++|+.+|..|++.|.+++|.|.++.|||.|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGEVVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSCCEEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeeeeeEecCcccCCCC
Confidence            5899999999999999999999999999999987

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.60  E-value=5.6e-09  Score=53.20  Aligned_cols=32  Identities=34%  Similarity=0.809  Sum_probs=29.6

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      .|.+|+++|+++.|+.+|++|||-+||.++|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            48899999999999999999999999998874

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=1.1e-08  Score=53.17  Aligned_cols=34  Identities=26%  Similarity=0.724  Sum_probs=29.6

Q ss_pred             ccccccCCCCCcccccccccccccccCceecccCC
Q psy3653          59 DDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        59 ~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      +||... ..+|..|+++|.++++.|.|+.|||.||
T Consensus         2 ~Cy~~t-lEkC~~C~~~I~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           2 GCYVAT-LEKCATCSQPILDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCSS-CCBCTTTCCBCCSCCEEETTEEECTTTC
T ss_pred             hhHHHH-HHHHHHhchHHHHHHHHHhCCCCCCCCC
Confidence            455443 4699999999999999999999999998

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.58  E-value=7e-09  Score=50.94  Aligned_cols=30  Identities=40%  Similarity=0.914  Sum_probs=28.2

Q ss_pred             ccccccccccCCCceeeeCCeeeccccccc
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFD   63 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~   63 (202)
                      |+|+.||+.|++.+...+||.+||+.||.+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            799999999999999999999999999965

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.55  E-value=1.8e-08  Score=50.43  Aligned_cols=31  Identities=29%  Similarity=0.761  Sum_probs=28.7

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      +|..|++.|. ++++.+||.|||..+|.+.||
T Consensus         1 kC~~C~~vL~-gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILT-GEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCS-SCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCcccc-ceeecCCCCcccHHHHHHhcC
Confidence            6899999997 579999999999999999998

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.53  E-value=1.7e-08  Score=56.33  Aligned_cols=37  Identities=43%  Similarity=0.931  Sum_probs=33.6

Q ss_pred             cccccccccCCCceeeeCCeeec-cccccccCCCCCcc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYC-RDDYFDLFAPKCGG   71 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC-~~c~~~~~~~~C~~   71 (202)
                      +|..|++.|++.+..++||+||| +.||.++|+|+=..
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~g   38 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFG   38 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCccc
Confidence            68999999999999999999999 78999999987544

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=2.2e-08  Score=54.71  Aligned_cols=32  Identities=31%  Similarity=0.822  Sum_probs=30.6

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      ||+.|++.|+.+.|...+|.+||+++|++||+
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~   32 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFK   32 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHH
Confidence            69999999999999999999999999999985

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.49  E-value=2.2e-08  Score=55.13  Aligned_cols=29  Identities=34%  Similarity=0.795  Sum_probs=27.2

Q ss_pred             CCCCCcccccccccccccccCceecccCC
Q psy3653          65 FAPKCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        65 ~~~~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      ..|+|+.|+++|.+++|.|+|+.||+++|
T Consensus        17 r~P~C~~C~~pI~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          17 RTPMCAHCNQVIRGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCCBBSSSCCBCCSCEEEETTEEECTTTC
T ss_pred             CCeeccccCCcccCceeeecCCccCcCCC
Confidence            35899999999999999999999999998

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.44  E-value=4.2e-08  Score=48.11  Aligned_cols=30  Identities=40%  Similarity=0.945  Sum_probs=28.6

Q ss_pred             ccccccccccCCCceEeeCCcccChhhHhh
Q psy3653         170 FVCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       170 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      |+|+.|++.|.+.....+||++||+.||.|
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            799999999999999999999999999986

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.41  E-value=4e-08  Score=49.26  Aligned_cols=32  Identities=31%  Similarity=0.777  Sum_probs=29.3

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      .|..|+++|+++.|..+|++|||-+||-++|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            48899999999999999999999999988764

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=1.3e-07  Score=48.10  Aligned_cols=34  Identities=38%  Similarity=0.681  Sum_probs=31.7

Q ss_pred             ccccccCCCCCCCCCCCcccceeeecCccccccc
Q psy3653         136 THYHAKRGSLCAGCHKPITGRCITAMFRKFHPEH  169 (202)
Q Consensus       136 ~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~H~~C  169 (202)
                      ++|+.+|+..|.+|.+.|+|.+++|...+|||+|
T Consensus         1 kdYw~kfge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             CcHHHHHHHHhhhhHhhcccceeeecccccCCCC
Confidence            3688899999999999999999999999999998

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=5.2e-08  Score=48.95  Aligned_cols=30  Identities=37%  Similarity=0.778  Sum_probs=26.8

Q ss_pred             ccCCCCCcccccccccccccccCceecccC
Q psy3653          63 DLFAPKCGGCNRAIMENYVSALNTQWHSTC   92 (202)
Q Consensus        63 ~~~~~~C~~C~~~I~~~~v~~~~~~~H~~C   92 (202)
                      +...|+|+.|++||.++++.|+++.||++.
T Consensus         2 kmg~p~C~~C~~PI~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           2 SMGVPICGACRRPIEGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCCEETTTTEECCSCEECCTTSBEETTT
T ss_pred             CcCCcchhhcCCchhhhHhhhhccccCCCC
Confidence            346789999999999999999999999863

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.36  E-value=1.1e-07  Score=47.90  Aligned_cols=31  Identities=23%  Similarity=0.736  Sum_probs=29.6

Q ss_pred             ccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         172 CAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       172 C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      |..|+++|++.+|..+++..||.+||++.|+
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCCceEeecchhhcC
Confidence            7899999999999999999999999999996

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=1.5e-07  Score=47.80  Aligned_cols=33  Identities=33%  Similarity=0.736  Sum_probs=31.9

Q ss_pred             ccccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         170 FVCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       170 f~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      |+|+.|.+++-+.+.+++.|..||..+|.++||
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhc
Confidence            789999999999999999999999999999998

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.33  E-value=1.4e-07  Score=47.44  Aligned_cols=31  Identities=29%  Similarity=0.748  Sum_probs=29.6

Q ss_pred             ccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         172 CAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       172 C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      |..|.++|+..+|..+++..||.+||++.|+
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCcEEEEeccccccC
Confidence            7899999999999999999999999999996

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.31  E-value=1.6e-07  Score=48.00  Aligned_cols=32  Identities=28%  Similarity=0.754  Sum_probs=29.3

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      .|..|.+++.+++|++.||+|||..+|-++-|
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~G   32 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRRG   32 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHHS
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhcC
Confidence            48999999999999999999999999987755

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.31  E-value=1.3e-07  Score=56.40  Aligned_cols=32  Identities=31%  Similarity=0.883  Sum_probs=30.3

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      .|..|++.|++....+++++|||+.||.++||
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fG   32 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYG   32 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHS
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccC
Confidence            38899999999999999999999999999998

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.28  E-value=7.8e-08  Score=49.14  Aligned_cols=31  Identities=32%  Similarity=0.790  Sum_probs=28.1

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLF   65 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~   65 (202)
                      +|.+|.+|+.+..|++.||+|||+.+|.++.
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhc
Confidence            5899999999999999999999999997653

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.27  E-value=2e-07  Score=46.36  Aligned_cols=31  Identities=29%  Similarity=0.857  Sum_probs=29.4

Q ss_pred             ccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         172 CAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       172 C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      |..|++.|++....++++++||+.||.+.||
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            6789999999999999999999999999998

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.26  E-value=1.2e-07  Score=56.56  Aligned_cols=39  Identities=23%  Similarity=0.526  Sum_probs=34.9

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCCCCCcccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCN   73 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~   73 (202)
                      .|..|++.|++.+..++|+++||+.||.++|+|+=.+=+
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~G   39 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKG   39 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccccc
Confidence            388999999999999999999999999999999866544

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.25  E-value=9.3e-08  Score=52.19  Aligned_cols=34  Identities=24%  Similarity=0.675  Sum_probs=31.7

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCCCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPK   68 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~   68 (202)
                      +|+.|++.|+..+|.+.+|.+||+++|.++|.++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhh
Confidence            6899999999999999999999999999999764

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=2.9e-07  Score=47.32  Aligned_cols=28  Identities=36%  Similarity=0.762  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      ...|++|++.| .++.+.|+++.||.+||
T Consensus         8 ~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           8 PSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             CccccccchhhhCCceeeeeecceeeeeC
Confidence            45799999999 78999999999999998

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.21  E-value=4.1e-07  Score=45.68  Aligned_cols=32  Identities=34%  Similarity=0.761  Sum_probs=29.9

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      .|+.|+++|..-.|++..|.+||..||++.|+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            48899999999999999999999999999986

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.19  E-value=4.1e-07  Score=45.39  Aligned_cols=28  Identities=18%  Similarity=0.451  Sum_probs=25.2

Q ss_pred             CCCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      .++|++|++++ ..+.+..+|+.||+.|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            46899999999 68889999999999885

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.18  E-value=3.5e-07  Score=46.06  Aligned_cols=32  Identities=41%  Similarity=0.912  Sum_probs=28.5

Q ss_pred             cccccccccCCCceeeeCCeeecc-ccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCR-DDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~-~c~~~~~~   66 (202)
                      +|..|++.|.+....++||+|||. +||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            588999999999999999999995 59988774

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.07  E-value=8.9e-07  Score=44.39  Aligned_cols=27  Identities=33%  Similarity=0.584  Sum_probs=23.8

Q ss_pred             CCCCCCCCCcccce-eeecCcccccccc
Q psy3653         144 SLCAGCHKPITGRC-ITAMFRKFHPEHF  170 (202)
Q Consensus       144 ~~C~~C~~~I~~~~-~~~~~~~~H~~Cf  170 (202)
                      ..|++|+++|.+++ +.+.++.||..|+
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            47999999999886 6899999999885

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.04  E-value=7.7e-07  Score=44.74  Aligned_cols=32  Identities=28%  Similarity=0.650  Sum_probs=29.3

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      .|..|.+||...+|+.+|+..||..||++.|+
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCCceEeecchhhcC
Confidence            37899999999999999999999999998774

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.04  E-value=1.1e-06  Score=42.99  Aligned_cols=25  Identities=40%  Similarity=0.897  Sum_probs=22.2

Q ss_pred             CCCCCCCcc----cceeeecCcccccccc
Q psy3653         146 CAGCHKPIT----GRCITAMFRKFHPEHF  170 (202)
Q Consensus       146 C~~C~~~I~----~~~~~~~~~~~H~~Cf  170 (202)
                      |+.|.+||+    +.+|...++.||.+||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            789999995    3679999999999998

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=2e-06  Score=43.63  Aligned_cols=34  Identities=26%  Similarity=0.686  Sum_probs=31.5

Q ss_pred             ccccccCCCCCcccccccccccccccCceecccC
Q psy3653          59 DDYFDLFAPKCGGCNRAIMENYVSALNTQWHSTC   92 (202)
Q Consensus        59 ~c~~~~~~~~C~~C~~~I~~~~v~~~~~~~H~~C   92 (202)
                      +||..+|+..|..|...|++.++.|.+..|||+|
T Consensus         1 kdYw~kfge~C~~C~~~itGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCSCCBCCTTCCBCTTS
T ss_pred             CcHHHHHHHHhhhhHhhcccceeeecccccCCCC
Confidence            4789999999999999999999999999999987

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.95  E-value=2.3e-06  Score=42.69  Aligned_cols=26  Identities=27%  Similarity=0.627  Sum_probs=23.1

Q ss_pred             CCCCCCCCCcccce-eeecCccccccc
Q psy3653         144 SLCAGCHKPITGRC-ITAMFRKFHPEH  169 (202)
Q Consensus       144 ~~C~~C~~~I~~~~-~~~~~~~~H~~C  169 (202)
                      ..|++|+++|.+++ +.+.++.||.+|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            56999999998886 689999999887

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.94  E-value=1.4e-06  Score=43.73  Aligned_cols=32  Identities=38%  Similarity=0.707  Sum_probs=28.8

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      .|+.|+.+|.+..|.+.+|++||+.||.+.++
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            48999999999999999999999999987653

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.94  E-value=1.6e-06  Score=43.47  Aligned_cols=32  Identities=31%  Similarity=0.749  Sum_probs=29.3

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      .|..|.+|+..++|+.+++..||.+||++.|+
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCcEEEEeccccccC
Confidence            37899999999999999999999999998774

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.91  E-value=3.4e-06  Score=44.09  Aligned_cols=29  Identities=24%  Similarity=0.429  Sum_probs=26.1

Q ss_pred             CCCCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         142 RGSLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       142 ~~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      ..++|..|++.| .-+.+.+.|+.||+.||
T Consensus         6 ~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           6 ARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            457899999999 67889999999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.91  E-value=2.7e-06  Score=41.76  Aligned_cols=27  Identities=22%  Similarity=0.460  Sum_probs=24.3

Q ss_pred             CCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         144 SLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       144 ~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      +.|++|++.+ ..+.+.-+++.||+.||
T Consensus         3 ~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcccccCCccccHHHhhhhHHHHhhccC
Confidence            6799999999 56779999999999998

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.90  E-value=2.8e-06  Score=41.36  Aligned_cols=25  Identities=40%  Similarity=0.859  Sum_probs=22.1

Q ss_pred             CCCCCCCccc----ceeeecCcccccccc
Q psy3653         146 CAGCHKPITG----RCITAMFRKFHPEHF  170 (202)
Q Consensus       146 C~~C~~~I~~----~~~~~~~~~~H~~Cf  170 (202)
                      |..|.+||++    .+|...++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            7889999953    679999999999998

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.90  E-value=2.6e-06  Score=43.10  Aligned_cols=34  Identities=38%  Similarity=0.815  Sum_probs=31.6

Q ss_pred             ccccccccccCCCceeeeCCeeeccccccccCCC
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAP   67 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~   67 (202)
                      |+|+.|.+|+-+...+++.|..||+..|.++|+.
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhcc
Confidence            7899999999888899999999999999999874

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.89  E-value=1.6e-06  Score=47.80  Aligned_cols=28  Identities=14%  Similarity=0.427  Sum_probs=25.4

Q ss_pred             CCCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      +++|.+|++.| ..|.+.+.|+.||+.||
T Consensus        15 ~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            47899999999 67788999999999998

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.85  E-value=2.6e-06  Score=42.22  Aligned_cols=31  Identities=23%  Similarity=0.566  Sum_probs=28.0

Q ss_pred             ccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          36 CAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        36 C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      |-.|++.|++++..++++++||+.||-+.++
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            6789999999999999999999999987764

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=3e-06  Score=41.80  Aligned_cols=29  Identities=28%  Similarity=0.708  Sum_probs=26.8

Q ss_pred             cccccccccCCCceeeeCCeeeccccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFD   63 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~   63 (202)
                      .|.+|+++|+++.|...+++.||-+||+.
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeecc
Confidence            48999999999999999999999999964

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.82  E-value=3.2e-06  Score=42.31  Aligned_cols=27  Identities=33%  Similarity=1.053  Sum_probs=23.9

Q ss_pred             CCCccccccccccc-ccccCceecccCC
Q psy3653          67 PKCGGCNRAIMENY-VSALNTQWHSTCF   93 (202)
Q Consensus        67 ~~C~~C~~~I~~~~-v~~~~~~~H~~Cf   93 (202)
                      ..|++|+++|.+++ +.++++.||..|+
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            57999999999985 5899999999885

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=6e-06  Score=40.68  Aligned_cols=29  Identities=31%  Similarity=0.843  Sum_probs=26.9

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      .|..|.+.|.+.+|...+++.||.+||+.
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeecc
Confidence            48899999999999999999999999964

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=6.1e-06  Score=43.27  Aligned_cols=29  Identities=28%  Similarity=0.427  Sum_probs=25.7

Q ss_pred             CCCCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         142 RGSLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       142 ~~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      ..++|..|++.| .-+.+.+.|+.||+.||
T Consensus         7 ~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           7 AGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             SSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            357899999999 56778999999999998

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.72  E-value=6.3e-06  Score=40.17  Aligned_cols=25  Identities=44%  Similarity=1.139  Sum_probs=22.2

Q ss_pred             Ccccccccc----cccccccCceecccCC
Q psy3653          69 CGGCNRAIM----ENYVSALNTQWHSTCF   93 (202)
Q Consensus        69 C~~C~~~I~----~~~v~~~~~~~H~~Cf   93 (202)
                      |+.|.+||+    .++|+..++.||..||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            788999997    3589999999999998

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.69  E-value=7.1e-06  Score=40.84  Aligned_cols=26  Identities=38%  Similarity=1.110  Sum_probs=23.1

Q ss_pred             CCCccccccccccc-ccccCceecccC
Q psy3653          67 PKCGGCNRAIMENY-VSALNTQWHSTC   92 (202)
Q Consensus        67 ~~C~~C~~~I~~~~-v~~~~~~~H~~C   92 (202)
                      ..|++|+++|.+++ +.+.++.||..|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            47999999999985 589999999887

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=1.2e-05  Score=39.92  Aligned_cols=28  Identities=36%  Similarity=0.918  Sum_probs=24.6

Q ss_pred             CCCCcccccccc-cccccccCceecccCC
Q psy3653          66 APKCGGCNRAIM-ENYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~-~~~v~~~~~~~H~~Cf   93 (202)
                      +++|++|+++++ .+.+.+.|+.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            579999999997 5778899999999885

>d1x62a2 g.39.1.3 (A:8-42) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.61  E-value=1.7e-05  Score=40.15  Aligned_cols=28  Identities=29%  Similarity=0.527  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCcccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      -+.|.+|+..|.|.+|.+.++.+||+||
T Consensus         8 lp~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             CccccccCCCcEeEEEEeccccCCCCCC
Confidence            4789999999999999999999999998

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.61  E-value=2e-05  Score=38.45  Aligned_cols=32  Identities=28%  Similarity=0.745  Sum_probs=29.8

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      .|+.|+..+++++|+.+....||..|.+..|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            48999999999999999999999999999885

>d1x62a2 g.39.1.3 (A:8-42) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=1.4e-05  Score=40.44  Aligned_cols=28  Identities=25%  Similarity=0.714  Sum_probs=26.4

Q ss_pred             CCCCcccccccccccccccCceecccCC
Q psy3653          66 APKCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      -|.|.+|+..|.+.++.++++.+||+||
T Consensus         8 lp~CdkCg~GIVG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSSCEECSSCEECTTTT
T ss_pred             CccccccCCCcEeEEEEeccccCCCCCC
Confidence            3789999999999999999999999997

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.58  E-value=1.7e-05  Score=38.87  Aligned_cols=28  Identities=32%  Similarity=0.975  Sum_probs=24.7

Q ss_pred             CCCCccccccccc-ccccccCceecccCC
Q psy3653          66 APKCGGCNRAIME-NYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~~-~~v~~~~~~~H~~Cf   93 (202)
                      .+.|++|++.+++ +.+.-.++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHHhhhhHHHHhhccC
Confidence            4789999999984 678889999999998

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=1.8e-05  Score=39.01  Aligned_cols=29  Identities=24%  Similarity=0.658  Sum_probs=26.6

Q ss_pred             cccccccccCCCceeeeCCeeeccccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFD   63 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~   63 (202)
                      .|.+|+..|.++.|+..+.+.||++||..
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeee
Confidence            48899999999999999999999999954

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.53  E-value=2.2e-05  Score=38.58  Aligned_cols=27  Identities=41%  Similarity=0.719  Sum_probs=24.9

Q ss_pred             CCCCCCCCCCcccceeeecCccccccc
Q psy3653         143 GSLCAGCHKPITGRCITAMFRKFHPEH  169 (202)
Q Consensus       143 ~~~C~~C~~~I~~~~~~~~~~~~H~~C  169 (202)
                      ..-|..|.+-|+++++.+.++.|||.|
T Consensus         5 ssgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           5 SSGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CCSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             cchhhhhhhhhhhhhhhccccccCCCC
Confidence            356999999999999999999999987

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.52  E-value=2.2e-05  Score=37.30  Aligned_cols=25  Identities=28%  Similarity=0.511  Sum_probs=21.8

Q ss_pred             CCCCCCCcc--cceeeecCcccccccc
Q psy3653         146 CAGCHKPIT--GRCITAMFRKFHPEHF  170 (202)
Q Consensus       146 C~~C~~~I~--~~~~~~~~~~~H~~Cf  170 (202)
                      |..|.+.|.  .+.+...|..||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            678999994  4678999999999998

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.50  E-value=1.5e-05  Score=40.09  Aligned_cols=27  Identities=22%  Similarity=0.490  Sum_probs=23.8

Q ss_pred             CCCCCCCCCc--ccceeeecCcccccccc
Q psy3653         144 SLCAGCHKPI--TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       144 ~~C~~C~~~I--~~~~~~~~~~~~H~~Cf  170 (202)
                      ..|++|++.|  .+.++.|.+..||..||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            4699999999  46678999999999998

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.49  E-value=2.6e-05  Score=42.09  Aligned_cols=28  Identities=36%  Similarity=0.587  Sum_probs=26.5

Q ss_pred             CCCCCCCCCCcccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      -+.|.+|+..|.|.+|.+.++.+|++||
T Consensus        18 LP~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             CccccccCCCcEEEEEEeccccCCCCCC
Confidence            4789999999999999999999999998

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.48  E-value=1.7e-05  Score=38.52  Aligned_cols=25  Identities=36%  Similarity=1.054  Sum_probs=21.9

Q ss_pred             Ccccccccc----cccccccCceecccCC
Q psy3653          69 CGGCNRAIM----ENYVSALNTQWHSTCF   93 (202)
Q Consensus        69 C~~C~~~I~----~~~v~~~~~~~H~~Cf   93 (202)
                      |..|.+||+    .++|+..++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            778999997    3588999999999997

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.46  E-value=1.9e-05  Score=37.96  Aligned_cols=26  Identities=12%  Similarity=0.390  Sum_probs=22.0

Q ss_pred             CCCCCCCCCc-ccceeeecCccccccc
Q psy3653         144 SLCAGCHKPI-TGRCITAMFRKFHPEH  169 (202)
Q Consensus       144 ~~C~~C~~~I-~~~~~~~~~~~~H~~C  169 (202)
                      ++|++|++.+ ..+.|.-.|+.||+.|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            5799999999 5677777899999987

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.45  E-value=2.7e-05  Score=42.03  Aligned_cols=28  Identities=32%  Similarity=0.695  Sum_probs=26.4

Q ss_pred             CCCCcccccccccccccccCceecccCC
Q psy3653          66 APKCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      -|.|.+|+..|.+.++.++++.+|++||
T Consensus        18 LP~CdkCg~GIVG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSCCEESSSCEECTTTC
T ss_pred             CccccccCCCcEEEEEEeccccCCCCCC
Confidence            3789999999999999999999999998

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.44  E-value=1.8e-05  Score=40.21  Aligned_cols=32  Identities=22%  Similarity=0.476  Sum_probs=27.9

Q ss_pred             cccccccccCCCceee-eCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHE-KDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~-~~g~~yC~~c~~~~~~   66 (202)
                      +|..|++.|++..|.+ .++++||-+||.+.|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            4789999999999985 7789999999998874

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.42  E-value=2.6e-05  Score=39.83  Aligned_cols=27  Identities=41%  Similarity=1.026  Sum_probs=24.6

Q ss_pred             CCCcccccccc-cccccccCceecccCC
Q psy3653          67 PKCGGCNRAIM-ENYVSALNTQWHSTCF   93 (202)
Q Consensus        67 ~~C~~C~~~I~-~~~v~~~~~~~H~~Cf   93 (202)
                      ..|++|++.|. ++.+.|+++.||.+||
T Consensus         9 ~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccccccchhhhCCceeeeeecceeeeeC
Confidence            47999999997 6788999999999998

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.39  E-value=4.1e-05  Score=36.28  Aligned_cols=25  Identities=20%  Similarity=0.506  Sum_probs=21.6

Q ss_pred             CCCCCCCcc--cceeeecCcccccccc
Q psy3653         146 CAGCHKPIT--GRCITAMFRKFHPEHF  170 (202)
Q Consensus       146 C~~C~~~I~--~~~~~~~~~~~H~~Cf  170 (202)
                      |..|.+.|.  .+.+...|..||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            678999994  4678999999999998

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.37  E-value=4.4e-05  Score=36.05  Aligned_cols=25  Identities=32%  Similarity=0.650  Sum_probs=20.9

Q ss_pred             CCCCCCCcc--cceeeecCcccccccc
Q psy3653         146 CAGCHKPIT--GRCITAMFRKFHPEHF  170 (202)
Q Consensus       146 C~~C~~~I~--~~~~~~~~~~~H~~Cf  170 (202)
                      |..|.+||.  ..-+...++.||..||
T Consensus         1 c~ecrkpigad~ke~h~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHYKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEETTEEEETTTC
T ss_pred             CccccCCcCcchHHhhccccccccccC
Confidence            678999994  4557889999999998

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.37  E-value=5.4e-05  Score=38.35  Aligned_cols=32  Identities=25%  Similarity=0.525  Sum_probs=28.5

Q ss_pred             cccccccccCCCceEee-CCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLNKGTFKEQ-NDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~-~~~~yC~~c~~~~fg  202 (202)
                      .|..|++.|.+-.|.+. ++++||.++|-+.|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            48899999999999864 789999999999986

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=3.9e-05  Score=37.69  Aligned_cols=26  Identities=23%  Similarity=0.663  Sum_probs=24.2

Q ss_pred             CCCcccccccccccccccCceecccC
Q psy3653          67 PKCGGCNRAIMENYVSALNTQWHSTC   92 (202)
Q Consensus        67 ~~C~~C~~~I~~~~v~~~~~~~H~~C   92 (202)
                      .-|..|.+.|++++++|.++.|||.|
T Consensus         6 sgC~~C~~~ItGkVLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSCCBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhhhhhccccccCCCC
Confidence            46999999999999999999999987

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.21  E-value=8.6e-05  Score=36.54  Aligned_cols=30  Identities=33%  Similarity=0.815  Sum_probs=27.0

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKL  200 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~  200 (202)
                      .|..|+..|.++.|+..+.+.||.+||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            488999999999999999999999999653

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.16  E-value=0.00011  Score=38.18  Aligned_cols=28  Identities=21%  Similarity=0.590  Sum_probs=24.8

Q ss_pred             CCCCccccccccc-ccccccCceecccCC
Q psy3653          66 APKCGGCNRAIME-NYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~~-~~v~~~~~~~H~~Cf   93 (202)
                      ..+|..|++.+.. +.+.+.|..||..||
T Consensus         7 ~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeEecCCeehhhccC
Confidence            4689999999984 678899999999998

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.15  E-value=4.9e-05  Score=41.59  Aligned_cols=27  Identities=30%  Similarity=0.821  Sum_probs=24.0

Q ss_pred             CCCcccccccc-cccccccCceecccCC
Q psy3653          67 PKCGGCNRAIM-ENYVSALNTQWHSTCF   93 (202)
Q Consensus        67 ~~C~~C~~~I~-~~~v~~~~~~~H~~Cf   93 (202)
                      ++|..|++.++ -+.+.+.|..||..||
T Consensus        16 ~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          16 DGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            58999999998 4677899999999998

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.11  E-value=0.00012  Score=38.16  Aligned_cols=28  Identities=18%  Similarity=0.507  Sum_probs=24.7

Q ss_pred             CCCCccccccccc-ccccccCceecccCC
Q psy3653          66 APKCGGCNRAIME-NYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~~-~~v~~~~~~~H~~Cf   93 (202)
                      +.+|..|++.+.. +.+.+.+..||..||
T Consensus         8 ~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeEEEecCcEeccccC
Confidence            4689999999984 678899999999998

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.09  E-value=7.7e-05  Score=37.37  Aligned_cols=26  Identities=31%  Similarity=0.715  Sum_probs=22.8

Q ss_pred             CCcccccccc--cccccccCceecccCC
Q psy3653          68 KCGGCNRAIM--ENYVSALNTQWHSTCF   93 (202)
Q Consensus        68 ~C~~C~~~I~--~~~v~~~~~~~H~~Cf   93 (202)
                      .|++|++.|.  +-++.|.+..||..||
T Consensus         4 ~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             ccccccCcCChhHhheecccceeeeccC
Confidence            6999999997  3477899999999998

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.06  E-value=0.00011  Score=34.91  Aligned_cols=25  Identities=36%  Similarity=0.969  Sum_probs=21.4

Q ss_pred             Ccccccccc--cccccccCceecccCC
Q psy3653          69 CGGCNRAIM--ENYVSALNTQWHSTCF   93 (202)
Q Consensus        69 C~~C~~~I~--~~~v~~~~~~~H~~Cf   93 (202)
                      |..|.+.|.  .+.+...|..||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            678999997  3578899999999998

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.99  E-value=0.00015  Score=34.32  Aligned_cols=25  Identities=28%  Similarity=0.873  Sum_probs=21.3

Q ss_pred             Ccccccccc--cccccccCceecccCC
Q psy3653          69 CGGCNRAIM--ENYVSALNTQWHSTCF   93 (202)
Q Consensus        69 C~~C~~~I~--~~~v~~~~~~~H~~Cf   93 (202)
                      |..|.+.|.  .+.+...|..||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            678999997  3578899999999998

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.99  E-value=0.00014  Score=34.26  Aligned_cols=25  Identities=40%  Similarity=0.834  Sum_probs=20.6

Q ss_pred             Ccccccccc--cccccccCceecccCC
Q psy3653          69 CGGCNRAIM--ENYVSALNTQWHSTCF   93 (202)
Q Consensus        69 C~~C~~~I~--~~~v~~~~~~~H~~Cf   93 (202)
                      |..|.+||.  .+-+...++.||..||
T Consensus         1 c~ecrkpigad~ke~h~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHYKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEETTEEEETTTC
T ss_pred             CccccCCcCcchHHhhccccccccccC
Confidence            678999997  3467788999999997

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=96.97  E-value=0.0002  Score=33.91  Aligned_cols=26  Identities=23%  Similarity=0.501  Sum_probs=23.3

Q ss_pred             CCCCCCCCc-ccceeeecCcccccccc
Q psy3653         145 LCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       145 ~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      +|..|.+.+ ..+-|.-.|+.||+.||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            689999999 57779999999999997

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.96  E-value=0.00013  Score=36.56  Aligned_cols=28  Identities=25%  Similarity=0.511  Sum_probs=24.8

Q ss_pred             CCCCCCCCCCc-ccceeeecCcccccccc
Q psy3653         143 GSLCAGCHKPI-TGRCITAMFRKFHPEHF  170 (202)
Q Consensus       143 ~~~C~~C~~~I-~~~~~~~~~~~~H~~Cf  170 (202)
                      +.+|..|++.+ ..+-|.-.|++||+.||
T Consensus         7 g~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CceeccccceEeeeeeeeecCcccccccC
Confidence            46899999999 57778999999999998

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.95  E-value=0.0002  Score=36.00  Aligned_cols=32  Identities=25%  Similarity=0.514  Sum_probs=28.2

Q ss_pred             cccccccccC--CCceEeeCCcccChhhHhhhcC
Q psy3653         171 VCAFCLRQLN--KGTFKEQNDKPYCHGCFEKLFG  202 (202)
Q Consensus       171 ~C~~C~~~l~--~~~~~~~~~~~yC~~c~~~~fg  202 (202)
                      +|+-|+.+|.  +.+.+.+.|.++|+.+|.++||
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhcC
Confidence            5788888887  5668999999999999999998

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.94  E-value=0.00018  Score=34.98  Aligned_cols=32  Identities=28%  Similarity=0.526  Sum_probs=28.4

Q ss_pred             cccccccccCCCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      +|+.|++.+.+.+|+.+....||-.|.+..|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            48999999999999999999999999877653

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.77  E-value=0.00043  Score=32.04  Aligned_cols=25  Identities=36%  Similarity=0.789  Sum_probs=21.3

Q ss_pred             CCCCCCCcc--cceeeecCcccccccc
Q psy3653         146 CAGCHKPIT--GRCITAMFRKFHPEHF  170 (202)
Q Consensus       146 C~~C~~~I~--~~~~~~~~~~~H~~Cf  170 (202)
                      |.+|++.+.  +..++++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            778999883  5568999999999997

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.70  E-value=0.00017  Score=36.24  Aligned_cols=32  Identities=38%  Similarity=0.779  Sum_probs=27.5

Q ss_pred             cccccccccC--CCceeeeCCeeeccccccccCC
Q psy3653          35 FCAQCGKQFG--EDGFHEKDGKPYCRDDYFDLFA   66 (202)
Q Consensus        35 ~C~~C~~~l~--~~~~~~~~g~~yC~~c~~~~~~   66 (202)
                      +|+-|+..|.  +.+.+.+.|.++|+.||.++|+
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhcC
Confidence            5788998886  4579999999999999988774

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.48  E-value=0.0007  Score=32.94  Aligned_cols=28  Identities=29%  Similarity=0.520  Sum_probs=25.1

Q ss_pred             cccccccccCCCceeeeCCeeecccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYF   62 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~   62 (202)
                      +|+.|-.||....|..+|+++.|..|..
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5889999999999999999999988753

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.43  E-value=0.00055  Score=33.50  Aligned_cols=28  Identities=25%  Similarity=0.683  Sum_probs=24.8

Q ss_pred             cccccccccCCCceeeeCCeeecccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYF   62 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~   62 (202)
                      .|+.|+.+|....++..++++||+....
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr   28 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHAR   28 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhh
Confidence            4899999999888999999999998754

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.32  E-value=0.0011  Score=32.20  Aligned_cols=28  Identities=36%  Similarity=0.753  Sum_probs=25.4

Q ss_pred             cccccccccCCCceEeeCCcccChhhHh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFE  198 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~  198 (202)
                      +|..|-.+|....|+.+|++++|..|-.
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            6888999999999999999999998864

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.22  E-value=0.0013  Score=32.90  Aligned_cols=31  Identities=26%  Similarity=0.718  Sum_probs=25.6

Q ss_pred             ccccccccccCCCc-eEe-eCCcccChhhHhhh
Q psy3653         170 FVCAFCLRQLNKGT-FKE-QNDKPYCHGCFEKL  200 (202)
Q Consensus       170 f~C~~C~~~l~~~~-~~~-~~~~~yC~~c~~~~  200 (202)
                      |.|..|+.-+++++ |.. ...++||..||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            78999999999777 553 46799999999874

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.13  E-value=0.0019  Score=31.36  Aligned_cols=29  Identities=31%  Similarity=0.716  Sum_probs=24.0

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEKL  200 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~~  200 (202)
                      .|+.|++.|.. .-.+..|.+||.+|..|+
T Consensus         1 nC~~Cgkelta-dArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTA-DARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCT-TCEEETTEEECHHHHHTT
T ss_pred             Cccccccccch-hHHHhcCCEEEEeccccc
Confidence            48899999874 467889999999999874

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=96.11  E-value=0.00082  Score=32.08  Aligned_cols=26  Identities=27%  Similarity=0.788  Sum_probs=20.6

Q ss_pred             CCCcccccccc-cccccccCceecccC
Q psy3653          67 PKCGGCNRAIM-ENYVSALNTQWHSTC   92 (202)
Q Consensus        67 ~~C~~C~~~I~-~~~v~~~~~~~H~~C   92 (202)
                      .+|.+|++.++ .+.+.-.|..||..|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            46899999998 455556789999876

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=95.48  E-value=0.002  Score=32.05  Aligned_cols=28  Identities=32%  Similarity=0.826  Sum_probs=23.8

Q ss_pred             CCCCcccccccc-cccccccCceecccCC
Q psy3653          66 APKCGGCNRAIM-ENYVSALNTQWHSTCF   93 (202)
Q Consensus        66 ~~~C~~C~~~I~-~~~v~~~~~~~H~~Cf   93 (202)
                      +.+|..|.+.++ .+-+.-.++.||..||
T Consensus         7 g~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CceeccccceEeeeeeeeecCcccccccC
Confidence            358999999997 6667889999999997

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.42  E-value=0.0065  Score=29.74  Aligned_cols=27  Identities=26%  Similarity=0.687  Sum_probs=22.8

Q ss_pred             cccccccccCCC-ceeeeCCeeeccccc
Q psy3653          35 FCAQCGKQFGED-GFHEKDGKPYCRDDY   61 (202)
Q Consensus        35 ~C~~C~~~l~~~-~~~~~~g~~yC~~c~   61 (202)
                      .|++|..+|.+. .|-..+|++||+.|-
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGC
T ss_pred             CcccccccccCCceeEEecCEEEEecCC
Confidence            489999998754 788999999999875

>d1x62a1 g.39.1.3 (A:43-73) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.32  E-value=0.00065  Score=33.29  Aligned_cols=28  Identities=21%  Similarity=0.629  Sum_probs=24.2

Q ss_pred             cccccccccCCCceeeeCCeeecccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYF   62 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~   62 (202)
                      .|+.|+.+|....++..++++||+....
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr   28 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHAR   28 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhh
Confidence            4899999998878999999999998754

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.32  E-value=0.0065  Score=29.56  Aligned_cols=29  Identities=24%  Similarity=0.406  Sum_probs=24.7

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      .|+.|+..|....++..++++||..+...
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhc
Confidence            48999999998888888999999987643

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=95.06  E-value=0.0043  Score=29.20  Aligned_cols=26  Identities=35%  Similarity=0.871  Sum_probs=22.1

Q ss_pred             CCcccccccc-cccccccCceecccCC
Q psy3653          68 KCGGCNRAIM-ENYVSALNTQWHSTCF   93 (202)
Q Consensus        68 ~C~~C~~~I~-~~~v~~~~~~~H~~Cf   93 (202)
                      +|..|.+.++ .+-+.-.++.||..||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            6888999987 5667889999999987

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.80  E-value=0.002  Score=32.48  Aligned_cols=25  Identities=20%  Similarity=0.344  Sum_probs=18.4

Q ss_pred             hHHhhCcCc------ccchhccccccccccc
Q psy3653           9 FDDHFSLRC------FQKCVTALEKTWHTEH   33 (202)
Q Consensus         9 ~~~~~~~~C------~~~~~~~~~~~~H~~C   33 (202)
                      +++..|.||      .++++...|..||+.|
T Consensus         5 L~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           5 LASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            345678888      3467778888888876

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.72  E-value=0.0089  Score=28.91  Aligned_cols=28  Identities=36%  Similarity=0.630  Sum_probs=23.4

Q ss_pred             cccccccccCCCceeeeCCeeeccccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFD   63 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~   63 (202)
                      .|+.|++.|..+ ..+..|.+||-+|..+
T Consensus         1 nC~~Cgkeltad-ArEl~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELTAD-ARELKGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCCTT-CEEETTEEECHHHHHT
T ss_pred             Cccccccccchh-HHHhcCCEEEEecccc
Confidence            378999999765 5688999999999765

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.62  E-value=0.014  Score=28.46  Aligned_cols=29  Identities=21%  Similarity=0.606  Sum_probs=26.4

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      +|..|+..|.+..|+-.-|+.+|.+|..+
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            68899999999999999999999999864

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.41  E-value=0.015  Score=29.17  Aligned_cols=27  Identities=11%  Similarity=0.361  Sum_probs=22.0

Q ss_pred             CCCCCCCCCCc--ccceeeecCccccccc
Q psy3653         143 GSLCAGCHKPI--TGRCITAMFRKFHPEH  169 (202)
Q Consensus       143 ~~~C~~C~~~I--~~~~~~~~~~~~H~~C  169 (202)
                      ...|.+|+...  .+..|...|..||..|
T Consensus         7 ~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           7 SATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHccCCCchHHhhcCCCccccccC
Confidence            45688898877  4677889999999987

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.01  E-value=0.016  Score=29.11  Aligned_cols=27  Identities=30%  Similarity=0.693  Sum_probs=24.4

Q ss_pred             CCCCCCCCCcccceeeecCcccccccc
Q psy3653         144 SLCAGCHKPITGRCITAMFRKFHPEHF  170 (202)
Q Consensus       144 ~~C~~C~~~I~~~~~~~~~~~~H~~Cf  170 (202)
                      ..|..|...|.++-+...|..||+..|
T Consensus         9 ~vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           9 YICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CBCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             HHHHHHHhhhhcCcceecCCCCCCCCC
Confidence            469999999988999999999999887

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.84  E-value=0.015  Score=29.25  Aligned_cols=26  Identities=27%  Similarity=0.465  Sum_probs=23.3

Q ss_pred             CCcccccccccccccccCceecccCC
Q psy3653          68 KCGGCNRAIMENYVSALNTQWHSTCF   93 (202)
Q Consensus        68 ~C~~C~~~I~~~~v~~~~~~~H~~Cf   93 (202)
                      .|..|...|.++.+.+.+..||+..|
T Consensus        10 vC~KCh~iIdd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2          10 ICQKCHAIIDEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             BCTTTCCBCCSCCCCCSSSCCCTTTS
T ss_pred             HHHHHHhhhhcCcceecCCCCCCCCC
Confidence            68889999988889999999999876

>d1x62a1 g.39.1.3 (A:43-73) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.69  E-value=0.0074  Score=29.40  Aligned_cols=29  Identities=24%  Similarity=0.403  Sum_probs=24.3

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      .|+.|+..|....++..++++||..+...
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            48899999998788888899999987643

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.54  E-value=0.018  Score=28.06  Aligned_cols=29  Identities=24%  Similarity=0.532  Sum_probs=25.9

Q ss_pred             cccccccccCCCceeeeCCeeeccccccc
Q psy3653          35 FCAQCGKQFGEDGFHEKDGKPYCRDDYFD   63 (202)
Q Consensus        35 ~C~~C~~~l~~~~~~~~~g~~yC~~c~~~   63 (202)
                      +|..|...|.+..|+-..|+.+|.+|..+
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            58899999999999999999999998754

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=93.32  E-value=0.026  Score=27.53  Aligned_cols=26  Identities=27%  Similarity=0.595  Sum_probs=21.9

Q ss_pred             cccccccccCCCc-eEeeCCcccChhh
Q psy3653         171 VCAFCLRQLNKGT-FKEQNDKPYCHGC  196 (202)
Q Consensus       171 ~C~~C~~~l~~~~-~~~~~~~~yC~~c  196 (202)
                      .|+.|..+|.+++ |-..+|.+||+..
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D   27 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHD   27 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGG
T ss_pred             CcccccccccCCceeEEecCEEEEecC
Confidence            4889999998776 8888999999865

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.11  E-value=0.025  Score=25.87  Aligned_cols=25  Identities=40%  Similarity=0.954  Sum_probs=19.9

Q ss_pred             Ccccccccc--cccccccCceecccCC
Q psy3653          69 CGGCNRAIM--ENYVSALNTQWHSTCF   93 (202)
Q Consensus        69 C~~C~~~I~--~~~v~~~~~~~H~~Cf   93 (202)
                      |.+|++.+.  +.-+.+.++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            677888876  3457789999999987

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.67  E-value=0.03  Score=27.30  Aligned_cols=27  Identities=30%  Similarity=0.568  Sum_probs=23.7

Q ss_pred             cccccccccCCCceEeeCCcccChhhH
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCF  197 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~  197 (202)
                      .|..|..+|.+..|...+..++|++|-
T Consensus         1 ncgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           1 NCGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             BCTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CCccceEEEEeeeeeeccCcEEehhcC
Confidence            377889999999999999999999885

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=92.39  E-value=0.03  Score=29.05  Aligned_cols=26  Identities=23%  Similarity=0.434  Sum_probs=18.0

Q ss_pred             CCCCCCCCc-cccee-eecCcccccccc
Q psy3653         145 LCAGCHKPI-TGRCI-TAMFRKFHPEHF  170 (202)
Q Consensus       145 ~C~~C~~~I-~~~~~-~~~~~~~H~~Cf  170 (202)
                      .|++|++.. .|+-+ .-.+.+|||.|-
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~   28 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACR   28 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHH
T ss_pred             CcchhhccccccceeeecCCceeCCccc
Confidence            388899888 34433 445678999874

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.20  E-value=0.074  Score=33.55  Aligned_cols=44  Identities=16%  Similarity=0.323  Sum_probs=34.2

Q ss_pred             ccccccccccCCCceeeeCCeeeccccccccCCCCCcccccccc
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYFDLFAPKCGGCNRAIM   77 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~~~~~~~C~~C~~~I~   77 (202)
                      ++|..|...+........=|..||..|..+.+...|..|+.++.
T Consensus        23 l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~   66 (97)
T d1jm7b_          23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAW   66 (97)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCS
T ss_pred             CCCccCCchhhcCceeCCCCCchhHHHHHHHHhccccccCCcCc
Confidence            68899988886653334568999999988887778888887765

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=91.08  E-value=0.026  Score=27.52  Aligned_cols=30  Identities=37%  Similarity=0.795  Sum_probs=24.1

Q ss_pred             ccccccccccCC--CceeeeCCeeeccccccc
Q psy3653          34 FFCAQCGKQFGE--DGFHEKDGKPYCRDDYFD   63 (202)
Q Consensus        34 f~C~~C~~~l~~--~~~~~~~g~~yC~~c~~~   63 (202)
                      ++|.-|+-+|.+  .+.+.+.+.+.|++||.+
T Consensus         1 LkC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           1 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             CccccccccccchhhHHHhhcceeeehhhhhc
Confidence            467778888875  367899999999999864

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.04  E-value=0.096  Score=25.43  Aligned_cols=26  Identities=19%  Similarity=0.597  Sum_probs=22.8

Q ss_pred             ccccccccCCCceeeeCCeeeccccc
Q psy3653          36 CAQCGKQFGEDGFHEKDGKPYCRDDY   61 (202)
Q Consensus        36 C~~C~~~l~~~~~~~~~g~~yC~~c~   61 (202)
                      |..|+-+|.++.|...+..++|++|-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhcC
Confidence            67888999999999999999998874

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.05  E-value=0.061  Score=26.67  Aligned_cols=30  Identities=17%  Similarity=0.453  Sum_probs=23.6

Q ss_pred             ccccccccccCCC-ceee-eCCeeeccccccc
Q psy3653          34 FFCAQCGKQFGED-GFHE-KDGKPYCRDDYFD   63 (202)
Q Consensus        34 f~C~~C~~~l~~~-~~~~-~~g~~yC~~c~~~   63 (202)
                      |.|..|+.-+.+. +|.. ...++||-.||.+
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~   32 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNE   32 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhc
Confidence            6799999988754 6774 5558999999875

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=89.45  E-value=0.13  Score=24.11  Aligned_cols=29  Identities=24%  Similarity=0.455  Sum_probs=24.1

Q ss_pred             cccccccccCCCceEeeCCcccChhhHhh
Q psy3653         171 VCAFCLRQLNKGTFKEQNDKPYCHGCFEK  199 (202)
Q Consensus       171 ~C~~C~~~l~~~~~~~~~~~~yC~~c~~~  199 (202)
                      .|..|..+|.+..|....+.++|.+|-..
T Consensus         1 nc~kcsvslvgrgflterddilc~dcgkd   29 (30)
T d1x4la2           1 NCKKCSLSLVGRGFLTERDDILCPDCGKD   29 (30)
T ss_dssp             BCSSSCCBCTTSCCEECSSSEECHHHHHT
T ss_pred             CcceeeEEEEeeeccccccceeccccCcC
Confidence            37788899998889888888999999654

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.83  E-value=0.3  Score=24.86  Aligned_cols=28  Identities=29%  Similarity=0.649  Sum_probs=15.6

Q ss_pred             ccccccccccCCCc-eEeeCCcccChhhH
Q psy3653         170 FVCAFCLRQLNKGT-FKEQNDKPYCHGCF  197 (202)
Q Consensus       170 f~C~~C~~~l~~~~-~~~~~~~~yC~~c~  197 (202)
                      |.|+.|.+++..++ ......+-.|..|-
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs   29 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCS   29 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHH
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcC
Confidence            56666666666555 33334455566554

>d2gvia2 g.39.1.18 (A:169-201) Uncharacterized protein Ta1109 {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: FwdE C-terminal domain-like
domain: Uncharacterized protein Ta1109
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=80.46  E-value=0.25  Score=23.45  Aligned_cols=29  Identities=34%  Similarity=0.740  Sum_probs=19.9

Q ss_pred             ccccccccccCCCceeeeCCeeecccccc
Q psy3653          34 FFCAQCGKQFGEDGFHEKDGKPYCRDDYF   62 (202)
Q Consensus        34 f~C~~C~~~l~~~~~~~~~g~~yC~~c~~   62 (202)
                      .+|..|+.---+..--.-+|+|.|+++|.
T Consensus         4 vrcdvcgeytyeadakllngkpvckpdyy   32 (33)
T d2gvia2           4 VRCDVCGEYTYEADAKLLNGKPVCKPDYY   32 (33)
T ss_dssp             EECTTTCCEEEGGGCEEETTEEECHHHHH
T ss_pred             eEEeeccceeeccchhhhCCCcccCcccC
Confidence            36778876543333446789999999874